401
|
Abstract
Sarcomere cardiomyopathies are genetic diseases that perturb contractile function and lead to hypertrophic or dilated myocardial remodeling. Identification of preclinical mutation carriers has yielded insights into the earliest biomechanical defects that link pathogenic variants to cardiac dysfunction. Understanding this early molecular pathophysiology can illuminate modifiable pathways to reduce the emergence of overt cardiomyopathy and curb adverse outcomes. Here, the authors review current understandings of how human hypertrophic cardiomyopathy- and hypertrophic dilated cardiomyopathy-linked mutations disrupt the normal structure and function of the sarcomere.
Collapse
Affiliation(s)
- Amanda C Garfinkel
- Department of Genetics, Harvard Medical School, New Research Building Room 256, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Jonathan G Seidman
- Department of Genetics, Harvard Medical School, New Research Building Room 256, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Christine E Seidman
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA 02115, USA; Department of Genetics, Brigham and Women's Hospital, Harvard Medical School, New Research Building Room 256, 77 Avenue Louis Pasteur, Boston, MA 02115, USA; Howard Hughes Medical Institute, 4000 Jones Bridge Road, Chevy Chase, MD 20815, USA.
| |
Collapse
|
402
|
Hershberger RE, Givertz MM, Ho CY, Judge DP, Kantor PF, McBride KL, Morales A, Taylor MRG, Vatta M, Ware SM. Genetic Evaluation of Cardiomyopathy-A Heart Failure Society of America Practice Guideline. J Card Fail 2018; 24:281-302. [PMID: 29567486 PMCID: PMC9903357 DOI: 10.1016/j.cardfail.2018.03.004] [Citation(s) in RCA: 256] [Impact Index Per Article: 42.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
This guideline describes the approach and expertise needed for the genetic evaluation of cardiomyopathy. First published in 2009 by the Heart Failure Society of America (HFSA), the guideline has now been updated in collaboration with the American College of Medical Genetics and Genomics (ACMG). The writing group, composed of cardiologists and genetics professionals with expertise in adult and pediatric cardiomyopathy, reflects the emergence and increased clinical activity devoted to cardiovascular genetic medicine. The genetic evaluation of cardiomyopathy is a rapidly emerging key clinical priority, because high-throughput sequencing is now feasible for clinical testing and conventional interventions can improve survival, reduce morbidity, and enhance quality of life. Moreover, specific interventions may be guided by genetic analysis. A systematic approach is recommended: always a comprehensive family history; an expert phenotypic evaluation of the proband and at-risk family members to confirm a diagnosis and guide genetic test selection and interpretation; referral to expert centers as needed; genetic testing, with pre- and post-test genetic counseling; and specific guidance as indicated for drug and device therapies. The evaluation of infants and children demands special expertise. The approach to managing secondary and incidental sequence findings as recommended by the ACMG is provided.
Collapse
Affiliation(s)
- Ray E Hershberger
- Division of Human Genetics, Ohio State University Wexner Medical Center, Columbus, Ohio; Division of Cardiovascular Medicine, Ohio State University Wexner Medical Center, Columbus, Ohio.
| | - Michael M Givertz
- Cardiovascular Division, Brigham and Women's Hospital, Boston, Massachusetts
| | - Carolyn Y Ho
- Cardiovascular Division, Brigham and Women's Hospital, Boston, Massachusetts
| | - Daniel P Judge
- Division of Cardiology, Medical University of South Carolina, Charleston, South Carolina
| | - Paul F Kantor
- Division of Pediatric Cardiology, University of Alberta and Stollery Children's Hospital, Edmonton, Canada
| | - Kim L McBride
- Center for Cardiovascular Research, Nationwide Children's Hospital, and Department of Pediatrics, Ohio State University, Columbus Ohio
| | - Ana Morales
- Division of Human Genetics, Ohio State University Wexner Medical Center, Columbus, Ohio
| | - Matthew R G Taylor
- Adult Medical Genetics Program, Division of Cardiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Matteo Vatta
- Invitae Corporation, San Francisco, California; Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana; Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana
| | - Stephanie M Ware
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana; Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana
| |
Collapse
|
403
|
Diao JA, Kohane IS, Manrai AK. Biomedical informatics and machine learning for clinical genomics. Hum Mol Genet 2018; 27:R29-R34. [PMID: 29566172 PMCID: PMC5946905 DOI: 10.1093/hmg/ddy088] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 03/08/2018] [Accepted: 03/08/2018] [Indexed: 12/22/2022] Open
Abstract
While tens of thousands of pathogenic variants are used to inform the many clinical applications of genomics, there remains limited information on quantitative disease risk for the majority of variants used in clinical practice. At the same time, rising demand for genetic counselling has prompted a growing need for computational approaches that can help interpret genetic variation. Such tasks include predicting variant pathogenicity and identifying variants that are too common to be penetrant. To address these challenges, researchers are increasingly turning to integrative informatics approaches. These approaches often leverage vast sources of data, including electronic health records and population-level allele frequency databases (e.g. gnomAD), as well as machine learning techniques such as support vector machines and deep learning. In this review, we highlight recent informatics and machine learning approaches that are improving our understanding of pathogenic variation and discuss obstacles that may limit their emerging role in clinical genomics.
Collapse
Affiliation(s)
- James A Diao
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
- Department of Statistics and Data Science, Yale University, New Haven, CT 06520, USA
| | - Isaac S Kohane
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Arjun K Manrai
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| |
Collapse
|
404
|
High-depth whole genome sequencing of an Ashkenazi Jewish reference panel: enhancing sensitivity, accuracy, and imputation. Hum Genet 2018; 137:343-355. [PMID: 29705978 DOI: 10.1007/s00439-018-1886-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Accepted: 04/21/2018] [Indexed: 12/31/2022]
Abstract
While increasingly large reference panels for genome-wide imputation have been recently made available, the degree to which imputation accuracy can be enhanced by population-specific reference panels remains an open question. Here, we sequenced at full-depth (≥ 30×), across two platforms (Illumina X Ten and Complete Genomics, Inc.), a moderately large (n = 738) cohort of samples drawn from the Ashkenazi Jewish population. We developed a series of quality control steps to optimize sensitivity, specificity, and comprehensiveness of variant calls in the reference panel, and then tested the accuracy of imputation against target cohorts drawn from the same population. Quality control (QC) thresholds for the Illumina X Ten platform were identified that permitted highly accurate calling of single nucleotide variants across 94% of the genome. QC procedures also identified numerous regions that are poorly mapped using current reference or alternate assemblies. After stringent QC, the population-specific reference panel produced more accurate and comprehensive imputation results relative to publicly available, large cosmopolitan reference panels, especially in the range of rare variants that may be most critical to further progress in mapping of complex phenotypes. The population-specific reference panel also permitted enhanced filtering of clinically irrelevant variants from personal genomes.
Collapse
|
405
|
Assessment of DNA repair susceptibility genes identified by whole exome sequencing in head and neck cancer. DNA Repair (Amst) 2018; 66-67:50-63. [PMID: 29747023 DOI: 10.1016/j.dnarep.2018.04.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 04/24/2018] [Accepted: 04/24/2018] [Indexed: 12/31/2022]
Abstract
Head and neck cancer (HNC), the sixth most common cancer globally, stands second in India. In Northeast (NE) India, it is the sixth most common cause of death in males and seventh in females. Prolonged tobacco and alcohol consumption constitute the major etiological factors for HNC development, which induce DNA damage. Therefore, DNA repair pathway is a crucial system in maintaining genomic integrity and preventing carcinogenesis. The present work was aimed to predict the consequence of significant germline variants of the DNA repair genes in disease predisposition. Whole exome sequencing was performed in Ion Proton™ platform on 15 case-control samples from the HNC-prevalent states of Manipur, Mizoram, and Nagaland. Variant annotation was done in Ion Reporter™ as well as wANNOVAR. Subsequent statistical and bioinformatics analysis identified significant exonic and intronic variants associated with HNC. Amongst our observed variants, 78.6% occurred in ExAC, 94% reported in dbSNP and 5.8% & 9.3% variants were present in ClinVar and HGMD, respectively. The total variants were dispersed among 199 genes with DSBR and FA pathway being the most mutated pathways. The allelic association test suggested that the intronic variants in HLTF and RAD52 gene significantly associated (P < 0.05) with the risk (OR > 5), while intronic variants in PARP4, RECQL5, EXO1 and PER1 genes and exonic variant in TDP2 gene showed protection (OR < 1) for HNC. MDR analysis proposed the exonic variants in MSH6, BRCA2, PALB2 and TP53 genes and intronic variant in RECQL5 genetic region working together during certain phase of DNA repair mechanism for HNC causation. In addition, other intronic and 3'UTR variations caused modifications in the transcription factor binding sites and miRNA target sites associated with HNC. Large-scale validation in NE Indian population, in-depth structure prediction and subsequent simulation of our recognized polymorphisms is necessary to identify true causal variants related to HNC.
Collapse
|
406
|
Despond EA, Dawson JF. Classifying Cardiac Actin Mutations Associated With Hypertrophic Cardiomyopathy. Front Physiol 2018; 9:405. [PMID: 29719515 PMCID: PMC5913282 DOI: 10.3389/fphys.2018.00405] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 04/04/2018] [Indexed: 11/13/2022] Open
Abstract
Mutations in the cardiac actin gene (ACTC1) are associated with the development of hypertrophic cardiomyopathy (HCM). To date, 12 different ACTC1 mutations have been discovered in patients with HCM. Given the high degree of sequence conservation of actin proteins and the range of protein–protein interactions actin participates in, mutations in cardiac actin leading to HCM are particularly interesting. Here, we suggest the classification of ACTC1 mutations based on the location of the resulting amino acid change in actin into three main groups: (1) those affecting only the binding site of the myosin molecular motor, termed M-class mutations, (2) those affecting only the binding site of the tropomyosin (Tm) regulatory protein, designated T-class mutations, and (3) those affecting both the myosin- and Tm-binding sites, called MT-class mutations. To understand the precise pathogenesis of cardiac actin mutations and develop treatments specific to the molecular cause of disease, we need to integrate rapidly growing structural information with studies of regulated actomyosin systems.
Collapse
Affiliation(s)
- Evan A Despond
- Department of Molecular and Cellular Biology, Centre for Cardiovascular Investigations, University of Guelph, Guelph, ON, Canada
| | - John F Dawson
- Department of Molecular and Cellular Biology, Centre for Cardiovascular Investigations, University of Guelph, Guelph, ON, Canada
| |
Collapse
|
407
|
Lorca R, Gómez J, Martín M, Cabanillas R, Calvo J, León V, Pascual I, Morís C, Coto E, R Reguero JJ. Insights Into Hypertrophic Cardiomyopathy Evaluation Through Follow-up of a Founder Pathogenic Variant. ACTA ACUST UNITED AC 2018; 72:138-144. [PMID: 29631964 DOI: 10.1016/j.rec.2018.02.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 01/22/2018] [Indexed: 10/17/2022]
Abstract
INTRODUCTION AND OBJECTIVES Hypertrophic cardiomyopathy (HCM) is the most common inherited cardiac disease. The current challenge relies on the accurate classification of the pathogenicity of the variants. Transthoracic echocardiography (TTE) is recommended at initial evaluation and cardiac magnetic resonance (CMR) imaging should also be considered. We aimed to reappraise the penetrance and clinical expression of the MYBPC3 p.G263* variant. METHODS Three hundred and eighty-four HCM probands and a control cohort of 450 individuals were studied for the main sarcomere genes by next-generation sequencing. All MYBPC3 p.G263* carriers were identified and family screening was performed. Clinical information was recorded retrospectively before 2015 and prospectively thereafter. Extra effort was invested in performing CMR in all carriers, despite TTE results. RESULTS Thirteen HCM probands and none of the controls were carriers of the MYBPC3 p.G263* pathogenic variant (according to the American College of Medical Genetics and Genomics and the Association for Molecular Pathology). A total of 39 carriers were identified with family screening. Most patients with HCM were asymptomatic at the time of diagnosis and showed late-onset disease. Despite having a relatively benign course in the young, late HCM-related complications could occur. Penetrance was around 70% when evaluated by TTE and was 87.2% with TTE plus CMR. Penetrance was age-dependent, reaching 100% in carriers older than 55 years. CONCLUSIONS MYBPC3 p.G263* shares with most truncating pathogenic variants in this gene a late onset, relatively benign clinical course in the young, and high penetrance. Cardiac magnetic resonance could be a useful tool to evaluate carriers despite TTE results.
Collapse
Affiliation(s)
- Rebeca Lorca
- Unidad de Cardiopatías Familiares, Departamento de Cardiología y Genética Molecular, Hospital Universitario Central de Asturias (HUCA), Oviedo, Asturias, Spain.
| | - Juan Gómez
- Unidad de Cardiopatías Familiares, Departamento de Cardiología y Genética Molecular, Hospital Universitario Central de Asturias (HUCA), Oviedo, Asturias, Spain
| | - María Martín
- Unidad de Cardiopatías Familiares, Departamento de Cardiología y Genética Molecular, Hospital Universitario Central de Asturias (HUCA), Oviedo, Asturias, Spain; Departamento de Biología Funcional, Universidad de Oviedo, Oviedo, Asturias, Spain
| | - Rubén Cabanillas
- Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA), Oviedo, Asturias, Spain
| | - Juan Calvo
- Departamento de Radiología, Hospital Universitario Central de Asturias (HUCA), Oviedo, Asturias, Spain
| | - Víctor León
- Unidad de Cardiopatías Familiares, Departamento de Cardiología y Genética Molecular, Hospital Universitario Central de Asturias (HUCA), Oviedo, Asturias, Spain
| | - Isaac Pascual
- Unidad de Cardiopatías Familiares, Departamento de Cardiología y Genética Molecular, Hospital Universitario Central de Asturias (HUCA), Oviedo, Asturias, Spain
| | - César Morís
- Unidad de Cardiopatías Familiares, Departamento de Cardiología y Genética Molecular, Hospital Universitario Central de Asturias (HUCA), Oviedo, Asturias, Spain; Instituto de Investigación Sanitaria del Principado de Asturias (IISPA), Oviedo, Asturias, Spain; Departamento de Medicina, Universidad de Oviedo, Oviedo, Asturias, Spain
| | - Eliecer Coto
- Unidad de Cardiopatías Familiares, Departamento de Cardiología y Genética Molecular, Hospital Universitario Central de Asturias (HUCA), Oviedo, Asturias, Spain; Instituto de Investigación Sanitaria del Principado de Asturias (IISPA), Oviedo, Asturias, Spain; Departamento de Medicina, Universidad de Oviedo, Oviedo, Asturias, Spain
| | - José Julián R Reguero
- Unidad de Cardiopatías Familiares, Departamento de Cardiología y Genética Molecular, Hospital Universitario Central de Asturias (HUCA), Oviedo, Asturias, Spain; Instituto de Investigación Sanitaria del Principado de Asturias (IISPA), Oviedo, Asturias, Spain
| |
Collapse
|
408
|
Affiliation(s)
- Luisa Mestroni
- University of Colorado-Cardiovascular Institute, University of Colorado Anschutz Medical Campus, Aurora (L.M.).
| | - Orfeo Sbaizero
- Department of Engineering and Architecture, University of Trieste, Italy (O.S.)
| |
Collapse
|
409
|
Ibanez L, Dube U, Davis AA, Fernandez MV, Budde J, Cooper B, Diez-Fairen M, Ortega-Cubero S, Pastor P, Perlmutter JS, Cruchaga C, Benitez BA. Pleiotropic Effects of Variants in Dementia Genes in Parkinson Disease. Front Neurosci 2018; 12:230. [PMID: 29692703 PMCID: PMC5902712 DOI: 10.3389/fnins.2018.00230] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 03/23/2018] [Indexed: 12/17/2022] Open
Abstract
Background: The prevalence of dementia in Parkinson disease (PD) increases dramatically with advancing age, approaching 80% in patients who survive 20 years with the disease. Increasing evidence suggests clinical, pathological and genetic overlap between Alzheimer disease, dementia with Lewy bodies and frontotemporal dementia with PD. However, the contribution of the dementia-causing genes to PD risk, cognitive impairment and dementia in PD is not fully established. Objective: To assess the contribution of coding variants in Mendelian dementia-causing genes on the risk of developing PD and the effect on cognitive performance of PD patients. Methods: We analyzed the coding regions of the amyloid-beta precursor protein (APP), Presenilin 1 and 2 (PSEN1, PSEN2), and Granulin (GRN) genes from 1,374 PD cases and 973 controls using pooled-DNA targeted sequence, human exome-chip and whole-exome sequencing (WES) data by single variant and gene base (SKAT-O and burden tests) analyses. Global cognitive function was assessed using the Mini-Mental State Examination (MMSE) or the Montreal Cognitive Assessment (MoCA). The effect of coding variants in dementia-causing genes on cognitive performance was tested by multiple regression analysis adjusting for gender, disease duration, age at dementia assessment, study site and APOE carrier status. Results: Known AD pathogenic mutations in the PSEN1 (p.A79V) and PSEN2 (p.V148I) genes were found in 0.3% of all PD patients. There was a significant burden of rare, likely damaging variants in the GRN and PSEN1 genes in PD patients when compared with frequencies in the European population from the ExAC database. Multiple regression analysis revealed that PD patients carrying rare variants in the APP, PSEN1, PSEN2, and GRN genes exhibit lower cognitive tests scores than non-carrier PD patients (p = 2.0 × 10-4), independent of age at PD diagnosis, age at evaluation, APOE status or recruitment site. Conclusions: Pathogenic mutations in the Alzheimer disease-causing genes (PSEN1 and PSEN2) are found in sporadic PD patients. PD patients with cognitive decline carry rare variants in dementia-causing genes. Variants in genes causing Mendelian neurodegenerative diseases exhibit pleiotropic effects.
Collapse
Affiliation(s)
- Laura Ibanez
- Department of Psychiatry, Washington University, Saint Louis, MO, United States
| | - Umber Dube
- Department of Psychiatry, Washington University, Saint Louis, MO, United States
| | - Albert A. Davis
- Department of Neurology, Washington University, Saint Louis, MO, United States
| | - Maria V. Fernandez
- Department of Psychiatry, Washington University, Saint Louis, MO, United States
| | - John Budde
- Department of Psychiatry, Washington University, Saint Louis, MO, United States
| | - Breanna Cooper
- Department of Psychiatry, Washington University, Saint Louis, MO, United States
| | - Monica Diez-Fairen
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas, Instituto de Salud Carlos III, Madrid, Spain
- Movement Disorders Unit, Department of Neurology, University Hospital Mutua de Terrassa, Fundació per la Recerca Biomèdica i Social Mútua Terrassa, Terrassa, Barcelona, Spain
| | - Sara Ortega-Cubero
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas, Instituto de Salud Carlos III, Madrid, Spain
- Department of Neurology and Neurosurgery, Hospital Universitario de Burgos, Burgos, Spain
| | - Pau Pastor
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas, Instituto de Salud Carlos III, Madrid, Spain
- Movement Disorders Unit, Department of Neurology, University Hospital Mutua de Terrassa, Fundació per la Recerca Biomèdica i Social Mútua Terrassa, Terrassa, Barcelona, Spain
| | - Joel S. Perlmutter
- Department of Neurology, Washington University, Saint Louis, MO, United States
- Departments of Radiology, Neuroscience, Physical Therapy, and Occupational Therapy, Washington University, Saint Louis, MO, United States
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University, Saint Louis, MO, United States
| | - Bruno A. Benitez
- Department of Medicine, Washington University, Saint Louis, MO, United States
| |
Collapse
|
410
|
Shah N, Hou YCC, Yu HC, Sainger R, Caskey CT, Venter JC, Telenti A. Identification of Misclassified ClinVar Variants via Disease Population Prevalence. Am J Hum Genet 2018; 102:609-619. [PMID: 29625023 DOI: 10.1016/j.ajhg.2018.02.019] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 02/22/2018] [Indexed: 01/07/2023] Open
Abstract
There is a significant interest in the standardized classification of human genetic variants. We used whole-genome sequence data from 10,495 unrelated individuals to contrast population frequency of pathogenic variants to the expected population prevalence of the disease. Analyses included the ACMG-recommended 59 gene-condition sets for incidental findings and 463 genes associated with 265 OrphaNet conditions. A total of 25,505 variants were used to identify patterns of inflation (i.e., excess genetic risk and misclassification). Inflation increases as the level of evidence supporting the pathogenic nature of the variant decreases. We observed up to 11.5% of genetic disorders with inflation in pathogenic variant sets and up to 92.3% for the variant set with conflicting interpretations. This improved to 7.7% and 57.7%, respectively, after filtering for disease-specific allele frequency. The patterns of inflation were replicated using public data from more than 138,000 genomes. The burden of rare variants was a main contributing factor of the observed inflation, indicating collective misclassified rare variants. We also analyzed the dynamics of re-classification of variant pathogenicity in ClinVar over time, which indicates progressive improvement in variant classification. The study shows that databases include a significant proportion of wrongly ascertained variants; however, it underscores the critical role of ClinVar to contrast claims and foster validation across submitters.
Collapse
|
411
|
Dainis AM, Ashley EA. Cardiovascular Precision Medicine in the Genomics Era. JACC Basic Transl Sci 2018; 3:313-326. [PMID: 30062216 PMCID: PMC6059349 DOI: 10.1016/j.jacbts.2018.01.003] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 12/31/2017] [Accepted: 01/02/2018] [Indexed: 12/20/2022]
Abstract
Precision medicine strives to delineate disease using multiple data sources-from genomics to digital health metrics-in order to be more precise and accurate in our diagnoses, definitions, and treatments of disease subtypes. By defining disease at a deeper level, we can treat patients based on an understanding of the molecular underpinnings of their presentations, rather than grouping patients into broad categories with one-size-fits-all treatments. In this review, the authors examine how precision medicine, specifically that surrounding genetic testing and genetic therapeutics, has begun to make strides in both common and rare cardiovascular diseases in the clinic and the laboratory, and how these advances are beginning to enable us to more effectively define risk, diagnose disease, and deliver therapeutics for each individual patient.
Collapse
Key Words
- CAD, coronary artery disease
- CF, cystic fibrosis
- CHD, coronary heart disease
- CML, chronic myelogenous leukemia
- CRS, conventional risk score
- CVD, cardiovascular disease
- CaM, calmodulin
- DCM, dilated cardiomyopathy
- DMD, Duchenne muscular dystrophy
- FH, familial hypercholesterolemia
- GRS, genomic risk score
- HCM, hypertrophic cardiomyopathy
- HDR, homology directed repair
- IVF, in vitro fertilization
- LDL-C, low-density lipoprotein cholesterol
- LQTS, long QT syndrome
- NGS, next-generation sequencing
- PGD, preimplantation genetic diagnosis
- SNP, single nucleotide polymorphism
- genome sequencing
- genomics
- iPSC, induced pluripotent stem cells
- precision medicine
- ssODN, single-stranded oligodeoxynucleotide
- targeted therapeutics
Collapse
Affiliation(s)
| | - Euan A. Ashley
- Department of Genetics, Stanford University, Stanford, California
- Department of Medicine, Stanford University, Stanford, California
- Stanford Center for Inherited Cardiovascular Disease, Stanford University, Stanford, California
| |
Collapse
|
412
|
Sheehan A, Messer AE, Papadaki M, Choudhry A, Kren V, Biedermann D, Blagg B, Khandelwal A, Marston SB. Molecular Defects in Cardiac Myofilament Ca 2+-Regulation Due to Cardiomyopathy-Linked Mutations Can Be Reversed by Small Molecules Binding to Troponin. Front Physiol 2018; 9:243. [PMID: 29636697 PMCID: PMC5881522 DOI: 10.3389/fphys.2018.00243] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 03/06/2018] [Indexed: 12/28/2022] Open
Abstract
The inherited cardiomyopathies, hypertrophic cardiomyopathy (HCM) and dilated cardiomyopathy (DCM) are relatively common, potentially life-threatening and currently untreatable. Mutations are often in the contractile proteins of cardiac muscle and cause abnormal Ca2+ regulation via troponin. HCM is usually linked to higher myofilament Ca2+-sensitivity whilst in both HCM and DCM mutant tissue there is often an uncoupling of the relationship between troponin I (TnI) phosphorylation by PKA and modulation of myofilament Ca2+-sensitivity, essential for normal responses to adrenaline. The adrenergic response is blunted, and this may predispose the heart to failure under stress. At present there are no compounds or interventions that can prevent or treat sarcomere cardiomyopathies. There is a need for novel therapies that act at a more fundamental level to affect the disease process. We demonstrated that epigallocatechin-3 gallate (EGCG) was found to be capable of restoring the coupled relationship between Ca2+-sensitivity and TnI phosphorylation in mutant thin filaments to normal in vitro, independent of the mutation (15 mutations tested). We have labeled this property "re-coupling." The action of EGCG in vitro to reverse the abnormality caused by myopathic mutations would appear to be an ideal pharmaceutical profile for treatment of inherited HCM and DCM but EGCG is known to be promiscuous in vivo and is thus unsuitable as a therapeutic drug. We therefore investigated whether other structurally related compounds can re-couple myofilaments without these off-target effects. We used the quantitative in vitro motility assay to screen 40 compounds, related to C-terminal Hsp90 inhibitors, and found 23 that can re-couple mutant myofilaments. There is no correlation between re-couplers and Hsp90 inhibitors. The Ca2+-sensitivity shift due to TnI phosphorylation was restored to 2.2 ± 0.01-fold (n = 19) compared to 2.0 ± 0.24-fold (n = 7) in wild-type thin filaments. Many of these compounds were either pure re-couplers or pure desensitizers, indicating these properties are independent; moreover, re-coupling ability could be lost with small changes of compound structure, indicating the possibility of specificity. Small molecules that can re-couple may have therapeutic potential. HIGHLIGHTS - Inherited cardiomyopathies are common diseases that are currently untreatable at a fundamental level and therefore finding a small molecule treatment is highly desirable.- We have identified a molecular level dysfunction common to nearly all mutations: uncoupling of the relationship between troponin I phosphorylation and modulation of myofilament Ca2+-sensitivity, essential for normal responses to adrenaline.- We have identified a new class of drugs that are capable of both reducing Ca2+-sensitivity and/or recouping the relationship between troponin I phosphorylation and Ca2+-sensitivity.- The re-coupling phenomenon can be explained on the basis of a single mechanism that is testable.- Measurements with a wide range of small molecules of varying structures can indicate the critical molecular features required for recoupling and allows the prediction of other potential re-couplers.
Collapse
Affiliation(s)
- Alice Sheehan
- NHLI, Imperial College London, London, United Kingdom
| | | | | | | | - Vladimír Kren
- Laboratory of Biotransformation, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
| | - David Biedermann
- Laboratory of Biotransformation, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
| | - Brian Blagg
- Department of Medicinal Chemistry, The University of Kansas, Lawrence, KS, United States
| | - Anuj Khandelwal
- Department of Medicinal Chemistry, The University of Kansas, Lawrence, KS, United States
| | | |
Collapse
|
413
|
Christensen KD, Vassy JL, Phillips KA, Blout CL, Azzariti DR, Lu CY, Robinson JO, Lee K, Douglas MP, Yeh JM, Machini K, Stout NK, Rehm HL, McGuire AL, Green RC, Dukhovny D. Short-term costs of integrating whole-genome sequencing into primary care and cardiology settings: a pilot randomized trial. Genet Med 2018; 20:1544-1553. [PMID: 29565423 PMCID: PMC6151171 DOI: 10.1038/gim.2018.35] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 01/30/2018] [Indexed: 12/26/2022] Open
Abstract
Purpose Great uncertainty exists about the costs associated with whole genome sequencing (WGS). Methods One hundred cardiology patients with cardiomyopathy diagnoses, and 100 ostensibly healthy primary care patients were randomized to receive a family history report alone or with a WGS report. Cardiology patients also reviewed prior genetic test results. WGS costs were estimated by tracking resource use and staff time. Downstream costs were estimated by identifying services in administrative data, medical records, and patient surveys for 6 months. Results The incremental cost per patient of WGS testing was $5,098 in cardiology settings and $5,073 in primary care settings compared to family history alone. Mean six month downstream costs did not differ statistically between the control and WGS arms in either setting (cardiology: difference = −$1,560, 95%CI −$7,558 to $3,866, p=0.36; primary care: difference = $681, 95%CI −$884 to $2,171, p=0.70). Scenario analyses showed the cost reduction of omitting or limiting the types of secondary findings was less than $69 and $182 per patient in cardiology and primary care, respectively. Conclusion Short-term costs of WGS were driven by the costs of sequencing and interpretation rather than downstream healthcare. Disclosing additional types of secondary findings has a limited cost impact following disclosure.
Collapse
Affiliation(s)
- Kurt D Christensen
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA. .,Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA.
| | - Jason L Vassy
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA.,Division of General Internal Medicine and Primary Care, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Section of General Internal Medicine, VA Boston Healthcare System, Boston, Massachusetts, USA
| | - Kathryn A Phillips
- Department of Clinical Pharmacy, Center for Translational and Policy Research on Personalized Medicine (TRANSPERS), University of California San Francisco, San Francisco, California, USA.,Philip R. Lee Institute for Health Policy and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, USA
| | - Carrie L Blout
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Danielle R Azzariti
- Partners HealthCare Laboratory for Molecular Medicine, Cambridge, Massachusetts, USA
| | - Christine Y Lu
- Department of Population Medicine, Harvard Pilgrim Health Care Institute, Boston, Massachusetts, USA.,Department of Population Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Jill O Robinson
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, Texas, USA
| | - Kaitlyn Lee
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, Texas, USA
| | - Michael P Douglas
- Department of Clinical Pharmacy, Center for Translational and Policy Research on Personalized Medicine (TRANSPERS), University of California San Francisco, San Francisco, California, USA
| | - Jennifer M Yeh
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA.,Division of General Pediatrics, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Kalotina Machini
- Partners HealthCare Laboratory for Molecular Medicine, Cambridge, Massachusetts, USA.,Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA.,Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Natasha K Stout
- Department of Population Medicine, Harvard Pilgrim Health Care Institute, Boston, Massachusetts, USA.,Department of Population Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Heidi L Rehm
- Partners HealthCare Laboratory for Molecular Medicine, Cambridge, Massachusetts, USA.,Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA.,Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Amy L McGuire
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, Texas, USA
| | - Robert C Green
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Partners HealthCare Personalized Medicine, Boston, Massachusetts, USA
| | - Dmitry Dukhovny
- Department of Pediatrics, Oregon Health & Science University, Portland, Oregon, USA
| | | |
Collapse
|
414
|
Benjamin EJ, Virani SS, Callaway CW, Chamberlain AM, Chang AR, Cheng S, Chiuve SE, Cushman M, Delling FN, Deo R, de Ferranti SD, Ferguson JF, Fornage M, Gillespie C, Isasi CR, Jiménez MC, Jordan LC, Judd SE, Lackland D, Lichtman JH, Lisabeth L, Liu S, Longenecker CT, Lutsey PL, Mackey JS, Matchar DB, Matsushita K, Mussolino ME, Nasir K, O'Flaherty M, Palaniappan LP, Pandey A, Pandey DK, Reeves MJ, Ritchey MD, Rodriguez CJ, Roth GA, Rosamond WD, Sampson UKA, Satou GM, Shah SH, Spartano NL, Tirschwell DL, Tsao CW, Voeks JH, Willey JZ, Wilkins JT, Wu JH, Alger HM, Wong SS, Muntner P. Heart Disease and Stroke Statistics-2018 Update: A Report From the American Heart Association. Circulation 2018; 137:e67-e492. [PMID: 29386200 DOI: 10.1161/cir.0000000000000558] [Citation(s) in RCA: 4513] [Impact Index Per Article: 752.2] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
|
415
|
Osborne AJ, Breno M, Borsa NG, Bu F, Frémeaux-Bacchi V, Gale DP, van den Heuvel LP, Kavanagh D, Noris M, Pinto S, Rallapalli PM, Remuzzi G, Rodríguez de Cordoba S, Ruiz A, Smith RJH, Vieira-Martins P, Volokhina E, Wilson V, Goodship THJ, Perkins SJ. Statistical Validation of Rare Complement Variants Provides Insights into the Molecular Basis of Atypical Hemolytic Uremic Syndrome and C3 Glomerulopathy. THE JOURNAL OF IMMUNOLOGY 2018; 200:2464-2478. [PMID: 29500241 DOI: 10.4049/jimmunol.1701695] [Citation(s) in RCA: 114] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 01/31/2018] [Indexed: 01/02/2023]
Abstract
Atypical hemolytic uremic syndrome (aHUS) and C3 glomerulopathy (C3G) are associated with dysregulation and overactivation of the complement alternative pathway. Typically, gene analysis for aHUS and C3G is undertaken in small patient numbers, yet it is unclear which genes most frequently predispose to aHUS or C3G. Accordingly, we performed a six-center analysis of 610 rare genetic variants in 13 mostly complement genes (CFH, CFI, CD46, C3, CFB, CFHR1, CFHR3, CFHR4, CFHR5, CFP, PLG, DGKE, and THBD) from >3500 patients with aHUS and C3G. We report 371 novel rare variants (RVs) for aHUS and 82 for C3G. Our new interactive Database of Complement Gene Variants was used to extract allele frequency data for these 13 genes using the Exome Aggregation Consortium server as the reference genome. For aHUS, significantly more protein-altering rare variation was found in five genes CFH, CFI, CD46, C3, and DGKE than in the Exome Aggregation Consortium (allele frequency < 0.01%), thus correlating these with aHUS. For C3G, an association was only found for RVs in C3 and the N-terminal C3b-binding or C-terminal nonsurface-associated regions of CFH In conclusion, the RV analyses showed nonrandom distributions over the affected proteins, and different distributions were observed between aHUS and C3G that clarify their phenotypes.
Collapse
Affiliation(s)
- Amy J Osborne
- Department of Structural and Molecular Biology, University College London, London WC1E 6BT, United Kingdom
| | - Matteo Breno
- Centro di Ricerche Cliniche per le Malattie Rare "Aldo e Cele Daccò," IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri," 24020 Ranica Bergamo, Italy
| | - Nicolo Ghiringhelli Borsa
- Molecular Otolaryngology and Renal Research Laboratories, Carver College of Medicine, University of Iowa, Iowa City, IA 52242
| | - Fengxiao Bu
- Molecular Otolaryngology and Renal Research Laboratories, Carver College of Medicine, University of Iowa, Iowa City, IA 52242.,Medical Genetics Center, Southwest Hospital, Chongqing 400038, China
| | - Véronique Frémeaux-Bacchi
- Assistance Publique-Hôpitaux de Paris, Hôpital Européen Georges Pompidou, Service d'Immunologie Biologique, 75015 Paris, France
| | - Daniel P Gale
- Centre for Nephrology, Royal Free Hospital, University College London, London NW3 2QG, United Kingdom
| | - Lambertus P van den Heuvel
- Department of Pediatric Nephrology, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands.,Department of Pediatric Nephrology, Department of Growth and Regeneration, University Hospital Leuven, 3000 Leuven, Belgium
| | - David Kavanagh
- The National Renal Complement Therapeutics Centre, Newcastle upon Tyne NE1 4LP, United Kingdom.,Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne NE1 3BZ, United Kingdom
| | - Marina Noris
- Centro di Ricerche Cliniche per le Malattie Rare "Aldo e Cele Daccò," IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri," 24020 Ranica Bergamo, Italy
| | - Sheila Pinto
- Department of Cellular and Molecular Medicine, Center for Biological Research and Center for Biomedical Network Research on Rare Diseases, 28040 Madrid, Spain
| | - Pavithra M Rallapalli
- Department of Structural and Molecular Biology, University College London, London WC1E 6BT, United Kingdom
| | - Giuseppe Remuzzi
- Centro di Ricerche Cliniche per le Malattie Rare "Aldo e Cele Daccò," IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri," 24020 Ranica Bergamo, Italy.,Department of Biomedical and Clinical Sciences, University of Milan, 20122 Milan, Italy; and
| | - Santiago Rodríguez de Cordoba
- Department of Cellular and Molecular Medicine, Center for Biological Research and Center for Biomedical Network Research on Rare Diseases, 28040 Madrid, Spain
| | - Angela Ruiz
- Department of Cellular and Molecular Medicine, Center for Biological Research and Center for Biomedical Network Research on Rare Diseases, 28040 Madrid, Spain
| | - Richard J H Smith
- Molecular Otolaryngology and Renal Research Laboratories, Carver College of Medicine, University of Iowa, Iowa City, IA 52242
| | - Paula Vieira-Martins
- Assistance Publique-Hôpitaux de Paris, Hôpital Européen Georges Pompidou, Service d'Immunologie Biologique, 75015 Paris, France
| | - Elena Volokhina
- Department of Pediatric Nephrology, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Valerie Wilson
- Northern Molecular Genetics Service, Newcastle upon Tyne Hospitals National Health Service Foundation Trust, Newcastle upon Tyne NE1 3BZ, United Kingdom
| | - Timothy H J Goodship
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne NE1 3BZ, United Kingdom
| | - Stephen J Perkins
- Department of Structural and Molecular Biology, University College London, London WC1E 6BT, United Kingdom;
| |
Collapse
|
416
|
Zigova M, Bernasovska J, Boronova I, Mydlarova Blascakova M, Kmec J. Finding the candidate sequence variants for diagnosis of hypertrophic cardiomyopathy in East Slovak patients. J Clin Lab Anal 2018; 32. [DOI: 10.1002/jcla.22303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 07/02/2017] [Indexed: 11/07/2022] Open
Affiliation(s)
- Michaela Zigova
- Department of Biology; Faculty of Humanities and Natural Sciences; University of Presov; Presov Slovakia
| | - Jarmila Bernasovska
- Department of Biology; Faculty of Humanities and Natural Sciences; University of Presov; Presov Slovakia
| | - Iveta Boronova
- Department of Biology; Faculty of Humanities and Natural Sciences; University of Presov; Presov Slovakia
| | - Marta Mydlarova Blascakova
- Department of Biology; Faculty of Humanities and Natural Sciences; University of Presov; Presov Slovakia
| | - Jan Kmec
- Department of Urgent Health Care; Faculty of Health Care; University of Presov; Presov Slovakia
- Cardiocentre; Faculty Hospital of J.A. Reiman; Presov Slovakia
| |
Collapse
|
417
|
Harakalova M, Asselbergs FW. Systems analysis of dilated cardiomyopathy in the next generation sequencing era. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2018; 10:e1419. [PMID: 29485202 DOI: 10.1002/wsbm.1419] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 12/31/2017] [Accepted: 01/17/2018] [Indexed: 12/17/2022]
Abstract
Dilated cardiomyopathy (DCM) is a form of severe failure of cardiac muscle caused by a long list of etiologies ranging from myocardial infarction, DNA mutations in cardiac genes, to toxics. Systems analysis integrating next-generation sequencing (NGS)-based omics approaches, such as the sequencing of DNA, RNA, and chromatin, provide valuable insights into DCM mechanisms. The outcome and interpretation of NGS methods can be affected by the localization of cardiac biopsy, level of tissue degradation, and variable ratios of different cell populations, especially in the presence of fibrosis. Heart tissue composition may even differ between sexes, or siblings carrying the same disease causing mutation. Therefore, before planning any experiments, it is important to fully appreciate the complexities of DCM, and the selection of samples suitable for given research question should be an interdisciplinary effort involving clinicians and biologists. The list of NGS omics datasets in DCM to date is short. More studies have to be performed to contribute to public data repositories and facilitate systems analysis. In addition, proper data integration is a difficult task requiring complex computational approaches. Despite these complications, there are multiple promising implications of systems analysis in DCM. By combining various types of datasets, for example, RNA-seq, ChIP-seq, or 4C, deep insights into cardiac biology, and possible biomarkers and treatment targets, can be gained. Systems analysis can also facilitate the annotation of noncoding mutations in cardiac-specific DNA regulatory regions that play a substantial role in maintaining the tissue- and cell-specific transcriptional programs in the heart. This article is categorized under: Physiology > Mammalian Physiology in Health and Disease Laboratory Methods and Technologies > Genetic/Genomic Methods Laboratory Methods and Technologies > RNA Methods.
Collapse
Affiliation(s)
- Magdalena Harakalova
- Department of Cardiology, Division Heart and Lungs, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Folkert W Asselbergs
- Department of Cardiology, Division Heart and Lungs, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands.,Durrer Center for Cardiovascular Research, Netherlands Heart Institute, Utrecht, Netherlands.,Institute of Cardiovascular Science, University College London, London, UK
| |
Collapse
|
418
|
Cassa CA, Jordan DM, Adzhubei I, Sunyaev S. A literature review at genome scale: improving clinical variant assessment. Genet Med 2018; 20:936-941. [PMID: 29388949 PMCID: PMC6070443 DOI: 10.1038/gim.2017.230] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 11/08/2017] [Indexed: 11/09/2022] Open
Abstract
PURPOSE Over 150,000 variants have been reported to cause Mendelian disease in the medical literature. It is still difficult to leverage this knowledge base in clinical practice, as many reports lack strong statistical evidence or may include false associations. Clinical laboratories assess whether these variants (along with newly observed variants that are adjacent to these published ones) underlie clinical disorders. METHODS We investigated whether citation data-including journal impact factor and the number of cited variants (NCV) in each gene with published disease associations-can be used to improve variant assessment. RESULTS Surprisingly, we found that impact factor is not predictive of pathogenicity, but the NCV score for each gene can provide statistical support for prediction of pathogenicity. When this gene-level citation metric is combined with variant-level evolutionary conservation and structural features, classification accuracy reaches 89.5%. Further, variants identified in clinical exome sequencing cases have higher NCVs than do simulated rare variants from the Exome Aggregation Consortium database within the same set of genes and functional consequences (P < 2.22 × 10-16). CONCLUSION Aggregate citation data can complement existing variant-based predictive algorithms, and can boost their performance without the need to access and review large numbers of papers. The NCV is a slow-growing metric of scientific knowledge about each gene's association with disease.
Collapse
Affiliation(s)
- Christopher A Cassa
- Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts, USA. .,Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA.
| | - Daniel M Jordan
- Department of Genetic and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ivan Adzhubei
- Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Shamil Sunyaev
- Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| |
Collapse
|
419
|
Whiffin N, Walsh R, Govind R, Edwards M, Ahmad M, Zhang X, Tayal U, Buchan R, Midwinter W, Wilk AE, Najgebauer H, Francis C, Wilkinson S, Monk T, Brett L, O'Regan DP, Prasad SK, Morris-Rosendahl DJ, Barton PJR, Edwards E, Ware JS, Cook SA. CardioClassifier: disease- and gene-specific computational decision support for clinical genome interpretation. Genet Med 2018; 20:1246-1254. [PMID: 29369293 DOI: 10.1038/gim.2017.258] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 12/05/2017] [Indexed: 11/10/2022] Open
Abstract
PURPOSE Internationally adopted variant interpretation guidelines from the American College of Medical Genetics and Genomics (ACMG) are generic and require disease-specific refinement. Here we developed CardioClassifier ( http://www.cardioclassifier.org ), a semiautomated decision-support tool for inherited cardiac conditions (ICCs). METHODS CardioClassifier integrates data retrieved from multiple sources with user-input case-specific information, through an interactive interface, to support variant interpretation. Combining disease- and gene-specific knowledge with variant observations in large cohorts of cases and controls, we refined 14 computational ACMG criteria and created three ICC-specific rules. RESULTS We benchmarked CardioClassifier on 57 expertly curated variants and show full retrieval of all computational data, concordantly activating 87.3% of rules. A generic annotation tool identified fewer than half as many clinically actionable variants (64/219 vs. 156/219, Fisher's P = 1.1 × 10-18), with important false positives, illustrating the critical importance of disease and gene-specific annotations. CardioClassifier identified putatively disease-causing variants in 33.7% of 327 cardiomyopathy cases, comparable with leading ICC laboratories. Through addition of manually curated data, variants found in over 40% of cardiomyopathy cases are fully annotated, without requiring additional user-input data. CONCLUSION CardioClassifier is an ICC-specific decision-support tool that integrates expertly curated computational annotations with case-specific data to generate fast, reproducible, and interactive variant pathogenicity reports, according to best practice guidelines.
Collapse
Affiliation(s)
- Nicola Whiffin
- National Heart & Lung Institute, Imperial College London, London, UK. .,Cardiovascular Research Centre at Royal Brompton and Harefield NHS Foundation Trust, London, UK. .,MRC London Institute of Medical Sciences, Imperial College London, London, UK.
| | - Roddy Walsh
- National Heart & Lung Institute, Imperial College London, London, UK.,Cardiovascular Research Centre at Royal Brompton and Harefield NHS Foundation Trust, London, UK
| | - Risha Govind
- National Heart & Lung Institute, Imperial College London, London, UK.,Cardiovascular Research Centre at Royal Brompton and Harefield NHS Foundation Trust, London, UK
| | - Matthew Edwards
- Clinical Genetics and Genomics Laboratory, Royal Brompton and Harefield NHS Foundation Trust, London, UK
| | - Mian Ahmad
- National Heart & Lung Institute, Imperial College London, London, UK.,Cardiovascular Research Centre at Royal Brompton and Harefield NHS Foundation Trust, London, UK
| | - Xiaolei Zhang
- National Heart & Lung Institute, Imperial College London, London, UK.,Cardiovascular Research Centre at Royal Brompton and Harefield NHS Foundation Trust, London, UK
| | - Upasana Tayal
- National Heart & Lung Institute, Imperial College London, London, UK.,Cardiovascular Research Centre at Royal Brompton and Harefield NHS Foundation Trust, London, UK
| | - Rachel Buchan
- National Heart & Lung Institute, Imperial College London, London, UK.,Cardiovascular Research Centre at Royal Brompton and Harefield NHS Foundation Trust, London, UK
| | - William Midwinter
- National Heart & Lung Institute, Imperial College London, London, UK.,Cardiovascular Research Centre at Royal Brompton and Harefield NHS Foundation Trust, London, UK
| | - Alicja E Wilk
- National Heart & Lung Institute, Imperial College London, London, UK.,Cardiovascular Research Centre at Royal Brompton and Harefield NHS Foundation Trust, London, UK
| | - Hanna Najgebauer
- National Heart & Lung Institute, Imperial College London, London, UK.,Cardiovascular Research Centre at Royal Brompton and Harefield NHS Foundation Trust, London, UK
| | - Catherine Francis
- National Heart & Lung Institute, Imperial College London, London, UK.,Cardiovascular Research Centre at Royal Brompton and Harefield NHS Foundation Trust, London, UK
| | - Sam Wilkinson
- Clinical Genetics and Genomics Laboratory, Royal Brompton and Harefield NHS Foundation Trust, London, UK
| | - Thomas Monk
- Clinical Genetics and Genomics Laboratory, Royal Brompton and Harefield NHS Foundation Trust, London, UK
| | - Laura Brett
- Clinical Genetics and Genomics Laboratory, Royal Brompton and Harefield NHS Foundation Trust, London, UK
| | - Declan P O'Regan
- MRC London Institute of Medical Sciences, Imperial College London, London, UK
| | - Sanjay K Prasad
- National Heart & Lung Institute, Imperial College London, London, UK.,Cardiovascular Research Centre at Royal Brompton and Harefield NHS Foundation Trust, London, UK
| | - Deborah J Morris-Rosendahl
- National Heart & Lung Institute, Imperial College London, London, UK.,Clinical Genetics and Genomics Laboratory, Royal Brompton and Harefield NHS Foundation Trust, London, UK
| | - Paul J R Barton
- National Heart & Lung Institute, Imperial College London, London, UK.,Cardiovascular Research Centre at Royal Brompton and Harefield NHS Foundation Trust, London, UK
| | - Elizabeth Edwards
- National Heart & Lung Institute, Imperial College London, London, UK.,Cardiovascular Research Centre at Royal Brompton and Harefield NHS Foundation Trust, London, UK
| | - James S Ware
- National Heart & Lung Institute, Imperial College London, London, UK.,Cardiovascular Research Centre at Royal Brompton and Harefield NHS Foundation Trust, London, UK.,MRC London Institute of Medical Sciences, Imperial College London, London, UK
| | - Stuart A Cook
- National Heart & Lung Institute, Imperial College London, London, UK.,Cardiovascular Research Centre at Royal Brompton and Harefield NHS Foundation Trust, London, UK.,National Heart Centre Singapore, Singapore, Singapore.,Duke-National University of Singapore, Singapore, Singapore
| |
Collapse
|
420
|
Burns C, Bagnall RD, Lam L, Semsarian C, Ingles J. Multiple Gene Variants in Hypertrophic Cardiomyopathy in the Era of Next-Generation Sequencing. ACTA ACUST UNITED AC 2018; 10:CIRCGENETICS.116.001666. [PMID: 28790153 DOI: 10.1161/circgenetics.116.001666] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2016] [Accepted: 05/15/2017] [Indexed: 12/19/2022]
Abstract
BACKGROUND Multiple likely pathogenic/pathogenic (LP/P; ≥2) variants in patients with hypertrophic cardiomyopathy were described 10 years ago with a prevalence of 5%. We sought to re-examine the significance of multiple rare variants in patients with hypertrophic cardiomyopathy in the setting of comprehensive and targeted panels. METHODS AND RESULTS Of 758 hypertrophic cardiomyopathy probands, we included 382 with ≥45 cardiomyopathy genes screened. There were 224 (59%) with ≥1 rare variant (allele frequency ≤0.02%). Variants were analyzed using varying sized gene panels to represent comprehensive or targeted testing. Based on a 45-gene panel, 127 (33%) had a LP/P variant, 139 (36%) had variants of uncertain significance, and 66 (17%) had multiple rare variants. A targeted 8-gene panel yielded 125 (32%) LP/P variants, 52 (14%) variants of uncertain significance, and 14 (4%) had multiple rare variants. No proband had 2 LP/P variants. Including affected family members (total n=412), cluster-adjusted analyses identified a phenotype effect, with younger age (odds ratio, 0.95; 95% confidence interval, 0.92-0.98; P=0.004) and family history of sudden cardiac death (odds ratio, 3.5; 95% confidence interval, 1.3-9.9; P=0.02) significantly more likely in multiple versus single variant patients when considering an 8-gene panel but not larger panels. Those with multiple variants had worse event-free survival from all-cause death, cardiac transplantation, and cardiac arrest (log-rank P=0.008). CONCLUSIONS No proband had multiple LP/P variants in contrast to previous reports. However, multiple rare variants regardless of classification were seen in 4% and contributed to earlier disease onset and cardiac events. Our findings support a cumulative variant hypothesis in hypertrophic cardiomyopathy.
Collapse
Affiliation(s)
- Charlotte Burns
- From the Agnes Ginges Centre for Molecular Cardiology, Centenary Institute, Sydney, New South Wales, Australia (C.B., R.D.B., L.L., C.S., J.I.); Central Clinical School, Sydney Medical School, University of Sydney, New South Wales, Australia (C.B., R.D.B., C.S., J.I.); and Department of Cardiology, Royal Prince Alfred Hospital, Sydney, New South Wales, Australia (C.B., C.S., J.I.)
| | - Richard D Bagnall
- From the Agnes Ginges Centre for Molecular Cardiology, Centenary Institute, Sydney, New South Wales, Australia (C.B., R.D.B., L.L., C.S., J.I.); Central Clinical School, Sydney Medical School, University of Sydney, New South Wales, Australia (C.B., R.D.B., C.S., J.I.); and Department of Cardiology, Royal Prince Alfred Hospital, Sydney, New South Wales, Australia (C.B., C.S., J.I.)
| | - Lien Lam
- From the Agnes Ginges Centre for Molecular Cardiology, Centenary Institute, Sydney, New South Wales, Australia (C.B., R.D.B., L.L., C.S., J.I.); Central Clinical School, Sydney Medical School, University of Sydney, New South Wales, Australia (C.B., R.D.B., C.S., J.I.); and Department of Cardiology, Royal Prince Alfred Hospital, Sydney, New South Wales, Australia (C.B., C.S., J.I.)
| | - Christopher Semsarian
- From the Agnes Ginges Centre for Molecular Cardiology, Centenary Institute, Sydney, New South Wales, Australia (C.B., R.D.B., L.L., C.S., J.I.); Central Clinical School, Sydney Medical School, University of Sydney, New South Wales, Australia (C.B., R.D.B., C.S., J.I.); and Department of Cardiology, Royal Prince Alfred Hospital, Sydney, New South Wales, Australia (C.B., C.S., J.I.)
| | - Jodie Ingles
- From the Agnes Ginges Centre for Molecular Cardiology, Centenary Institute, Sydney, New South Wales, Australia (C.B., R.D.B., L.L., C.S., J.I.); Central Clinical School, Sydney Medical School, University of Sydney, New South Wales, Australia (C.B., R.D.B., C.S., J.I.); and Department of Cardiology, Royal Prince Alfred Hospital, Sydney, New South Wales, Australia (C.B., C.S., J.I.).
| |
Collapse
|
421
|
Miszalski-Jamka K, Jefferies JL, Mazur W, Głowacki J, Hu J, Lazar M, Gibbs RA, Liczko J, Kłyś J, Venner E, Muzny DM, Rycaj J, Białkowski J, Kluczewska E, Kalarus Z, Jhangiani S, Al-Khalidi H, Kukulski T, Lupski JR, Craigen WJ, Bainbridge MN. Novel Genetic Triggers and Genotype-Phenotype Correlations in Patients With Left Ventricular Noncompaction. ACTA ACUST UNITED AC 2018; 10:CIRCGENETICS.117.001763. [PMID: 28798025 DOI: 10.1161/circgenetics.117.001763] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 05/15/2017] [Indexed: 01/14/2023]
Abstract
BACKGROUND Left ventricular noncompaction (LVNC) is a genetically and phenotypically heterogeneous disease and, although increasingly recognized in clinical practice, there is a lack of widely accepted diagnostic criteria. We sought to identify novel genetic causes of LVNC and describe genotype-phenotype correlations. METHODS AND RESULTS A total of 190 patients from 174 families with left ventricular hypertrabeculation (LVHT) or LVNC were referred for cardiac magnetic resonance and whole-exome sequencing. A total of 425 control individuals were included to identify variants of interest (VOIs). We found an excess of 138 VOIs in 102 (59%) unrelated patients in 54 previously identified LVNC or other known cardiomyopathy genes. VOIs were found in 68 of 90 probands with LVNC and 34 of 84 probands with LVHT (76% and 40%, respectively; P<0.001). We identified 0, 1, and ≥2 VOIs in 72, 74, and 28 probands, respectively. We found increasing number of VOIs in a patient strongly correlated with several markers of disease severity, including ratio of noncompacted to compacted myocardium (P<0.001) and left ventricular ejection fraction (P=0.01). The presence of sarcomeric gene mutations was associated with increased occurrence of late gadolinium enhancement (P=0.004). CONCLUSIONS LVHT and LVNC likely represent a continuum of genotypic disease with differences in severity and variable phenotype explained, in part, by the number of VOIs and whether mutations are present in sarcomeric or nonsarcomeric genes. Presence of VOIs is common in patients with LVHT. Our findings expand the current clinical and genetic diagnostic approaches for patients with LVHT and LVNC.
Collapse
|
422
|
Kelly MA, Caleshu C, Morales A, Buchan J, Wolf Z, Harrison SM, Cook S, Dillon MW, Garcia J, Haverfield E, Jongbloed JDH, Macaya D, Manrai A, Orland K, Richard G, Spoonamore K, Thomas M, Thomson K, Vincent LM, Walsh R, Watkins H, Whiffin N, Ingles J, van Tintelen JP, Semsarian C, Ware JS, Hershberger R, Funke B. Adaptation and validation of the ACMG/AMP variant classification framework for MYH7-associated inherited cardiomyopathies: recommendations by ClinGen's Inherited Cardiomyopathy Expert Panel. Genet Med 2018; 20:351-359. [PMID: 29300372 PMCID: PMC5876064 DOI: 10.1038/gim.2017.218] [Citation(s) in RCA: 238] [Impact Index Per Article: 39.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 10/24/2017] [Indexed: 01/20/2023] Open
Abstract
Purpose Integrating genomic sequencing in clinical care requires standardization of variant interpretation practices. The Clinical Genome Resource has established expert panels to adapt the American College of Medical Genetics and Genomics/Association for Molecular Pathology classification framework for specific genes and diseases. The Cardiomyopathy Expert Panel selected MYH7, a key contributor to inherited cardiomyopathies, as a pilot gene to develop a broadly applicable approach. Methods Expert revisions were tested with 60 variants using a structured double review by pairs of clinical and diagnostic laboratory experts. Final consensus rules were established via iterative discussions. Results Adjustments represented disease-/gene-informed specifications (12) or strength adjustments of existing rules (5). Nine rules were deemed not applicable. Key specifications included quantitative frameworks for minor allele frequency thresholds, the use of segregation data, and a semiquantitative approach to counting multiple independent variant occurrences where fully controlled case-control studies are lacking. Initial inter-expert classification concordance was 93%. Internal data from participating diagnostic laboratories changed the classification of 20% of the variants (n = 12), highlighting the critical importance of data sharing. Conclusion These adapted rules provide increased specificity for use in MYH7-associated disorders in combination with expert review and clinical judgment and serve as a stepping stone for genes and disorders with similar genetic and clinical characteristics.
Collapse
Affiliation(s)
- Melissa A Kelly
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Boston, Massachusetts, USA
| | - Colleen Caleshu
- Stanford Center for Inherited Cardiovascular Disease, Stanford University, Stanford, California, USA
| | - Ana Morales
- Division of Human Genetics, Department of Internal Medicine, Ohio State University, Columbus, Ohio, USA
| | - Jillian Buchan
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Boston, Massachusetts, USA
| | - Zena Wolf
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Boston, Massachusetts, USA
| | - Steven M Harrison
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Boston, Massachusetts, USA
| | - Stuart Cook
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Mitchell W Dillon
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Boston, Massachusetts, USA
| | - John Garcia
- Invitae Inc., San Francisco, California, USA
| | | | - Jan D H Jongbloed
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | | | - Arjun Manrai
- Harvard School of Public Health, Boston, Massachusetts, USA
| | - Kate Orland
- Clinical Science Center, University of Wisconsin, Madison, Wisconsin, USA
| | | | - Katherine Spoonamore
- Krannert Institute of Cardiology, Indiana University, Indianapolis, Indiana, USA
| | - Matthew Thomas
- Division of Genetics, Department of Pediatrics, University of Virginia, Charlottesville, Virginia, USA
| | - Kate Thomson
- Oxford Medical Genetics Laboratory, Oxford University Hospitals NHS Foundation Trust, The Churchill Hospital, Oxford, UK.,Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | | | - Roddy Walsh
- National Heart and Lung Institute, Imperial College London, London, UK.,Royal Brompton & Harefield Hospitals NHS Trust, London, UK
| | - Hugh Watkins
- Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Nicola Whiffin
- National Heart and Lung Institute, Imperial College London, London, UK.,Royal Brompton & Harefield Hospitals NHS Trust, London, UK
| | - Jodie Ingles
- Agnes Ginges Centre for Molecular Cardiology, Centenary Institute and University of Sydney, Sydney, Australia
| | - J Peter van Tintelen
- Department of Clinical Genetics, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Christopher Semsarian
- Agnes Ginges Centre for Molecular Cardiology, Centenary Institute and University of Sydney, Sydney, Australia
| | - James S Ware
- National Heart and Lung Institute, Imperial College London, London, UK.,Royal Brompton & Harefield Hospitals NHS Trust, London, UK
| | - Ray Hershberger
- Division of Human Genetics, Department of Internal Medicine, Ohio State University, Columbus, Ohio, USA
| | - Birgit Funke
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Boston, Massachusetts, USA.,Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| |
Collapse
|
423
|
Abstract
In humans, dominant mutations in the gene encoding the regulatory γ2-subunit of AMP-activated protein kinase (PRKAG2) result in a highly penetrant phenotype dominated by cardiac features: left ventricular hypertrophy, ventricular pre-excitation, atrial tachyarrhythmia, cardiac conduction disease, and myocardial glycogen storage. The discovery of a link between the cell's fundamental energy sensor, AMPK, and inherited cardiac disease catalyzed intense interest into the biological role of AMPK in the heart. In this chapter, we provide an introduction to the spectrum of human disease resulting from pathogenic variants in PRKAG2, outlining its discovery, clinical genetics, and current perspectives on its pathogenesis and highlighting mechanistic insights derived through the evaluation of disease models. We also present a clinical perspective on the major components of the cardiomyopathy associated with mutations in PRKAG2, together with less commonly described extracardiac features, its prognosis, and principles of management.
Collapse
Affiliation(s)
- Arash Yavari
- Experimental Therapeutics, Radcliffe Department of Medicine, University of Oxford, Oxford, UK. .,Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK. .,The Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
| | - Dhruv Sarma
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.,The Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Eduardo B Sternick
- Instituto de Pós-Graduação, Faculdade de Ciências Médicas de Minas Gerais, Belo Horizonte, Brazil
| |
Collapse
|
424
|
Abstract
Dilated cardiomyopathy (DCM) affects approximately 1 in 250 individuals and is the leading indication for heart transplantation. DCM is often familial, and the most common genetic predisposition is a truncating variation in the giant sarcomeric protein, titin, which occurs in up to 15% of ambulant patients with DCM and 25% of end-stage or familial cases. In this article, we review the evidence for the role of titin truncation in the pathogenesis of DCM and our understanding of the molecular mechanisms and pathophysiological consequences of variation in the gene encoding titin (TTN). Such variation is common in the general population (up to 1% of individuals), and we consider key features that discriminate variants with disease-causing potential from those that are benign. We summarize strategies for clinical interpretation of genetic variants for use in the diagnosis of patients and the evaluation of their relatives. Finally, we consider the contemporary and potential future role for genetic stratification in cardiomyopathy and in the general population, evaluating titin variation as a predictor of outcome and treatment response for precision medicine.
Collapse
Affiliation(s)
- James S Ware
- National Heart and Lung Institute, Imperial College London, Royal Brompton Hospital, Sydney Street, London SW3 6NP, UK.,Medical Research College (MRC) London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK
| | - Stuart A Cook
- National Heart and Lung Institute, Imperial College London, Royal Brompton Hospital, Sydney Street, London SW3 6NP, UK.,Medical Research College (MRC) London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK.,Duke-National University of Singapore (Duke-NUS) Medical School and National Heart Centre Singapore, 8 College Road, 169857, Singapore
| |
Collapse
|
425
|
Reuter C, Grove ME, Orland K, Spoonamore K, Caleshu C. Clinical Cardiovascular Genetic Counselors Take a Leading Role in Team-based Variant Classification. J Genet Couns 2017; 27:751-760. [DOI: 10.1007/s10897-017-0175-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 11/07/2017] [Indexed: 01/08/2023]
|
426
|
Miller EM, Hinton RB, Czosek R, Lorts A, Parrott A, Shikany AR, Ittenbach RF, Ware SM. Genetic Testing in Pediatric Left Ventricular Noncompaction. ACTA ACUST UNITED AC 2017; 10:CIRCGENETICS.117.001735. [DOI: 10.1161/circgenetics.117.001735] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 09/20/2017] [Indexed: 11/16/2022]
Affiliation(s)
- Erin M. Miller
- From the Division of Cardiology (E.M.M., R.B.H., R.C., A.L., A.P., A.R.S.) and Division of Biostatistics and Epidemiology (R.F.I.), Cincinnati Children’s Hospital Medical Center, OH; and Department of Pediatrics and Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis (S.M.W.)
| | - Robert B. Hinton
- From the Division of Cardiology (E.M.M., R.B.H., R.C., A.L., A.P., A.R.S.) and Division of Biostatistics and Epidemiology (R.F.I.), Cincinnati Children’s Hospital Medical Center, OH; and Department of Pediatrics and Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis (S.M.W.)
| | - Richard Czosek
- From the Division of Cardiology (E.M.M., R.B.H., R.C., A.L., A.P., A.R.S.) and Division of Biostatistics and Epidemiology (R.F.I.), Cincinnati Children’s Hospital Medical Center, OH; and Department of Pediatrics and Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis (S.M.W.)
| | - Angela Lorts
- From the Division of Cardiology (E.M.M., R.B.H., R.C., A.L., A.P., A.R.S.) and Division of Biostatistics and Epidemiology (R.F.I.), Cincinnati Children’s Hospital Medical Center, OH; and Department of Pediatrics and Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis (S.M.W.)
| | - Ashley Parrott
- From the Division of Cardiology (E.M.M., R.B.H., R.C., A.L., A.P., A.R.S.) and Division of Biostatistics and Epidemiology (R.F.I.), Cincinnati Children’s Hospital Medical Center, OH; and Department of Pediatrics and Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis (S.M.W.)
| | - Amy R. Shikany
- From the Division of Cardiology (E.M.M., R.B.H., R.C., A.L., A.P., A.R.S.) and Division of Biostatistics and Epidemiology (R.F.I.), Cincinnati Children’s Hospital Medical Center, OH; and Department of Pediatrics and Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis (S.M.W.)
| | - Richard F. Ittenbach
- From the Division of Cardiology (E.M.M., R.B.H., R.C., A.L., A.P., A.R.S.) and Division of Biostatistics and Epidemiology (R.F.I.), Cincinnati Children’s Hospital Medical Center, OH; and Department of Pediatrics and Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis (S.M.W.)
| | - Stephanie M. Ware
- From the Division of Cardiology (E.M.M., R.B.H., R.C., A.L., A.P., A.R.S.) and Division of Biostatistics and Epidemiology (R.F.I.), Cincinnati Children’s Hospital Medical Center, OH; and Department of Pediatrics and Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis (S.M.W.)
| |
Collapse
|
427
|
Cardoso L, Stevenson M, Thakker RV. Molecular genetics of syndromic and non-syndromic forms of parathyroid carcinoma. Hum Mutat 2017; 38:1621-1648. [PMID: 28881068 PMCID: PMC5698716 DOI: 10.1002/humu.23337] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Revised: 08/21/2017] [Accepted: 09/04/2017] [Indexed: 12/23/2022]
Abstract
Parathyroid carcinoma (PC) may occur as part of a complex hereditary syndrome or an isolated (i.e., non-syndromic) non-hereditary (i.e., sporadic) endocrinopathy. Studies of hereditary and syndromic forms of PC, which include the hyperparathyroidism-jaw tumor syndrome (HPT-JT), multiple endocrine neoplasia types 1 and 2 (MEN1 and MEN2), and familial isolated primary hyperparathyroidism (FIHP), have revealed some genetic mechanisms underlying PC. Thus, cell division cycle 73 (CDC73) germline mutations cause HPT-JT, and CDC73 mutations occur in 70% of sporadic PC, but in only ∼2% of parathyroid adenomas. Moreover, CDC73 germline mutations occur in 20%-40% of patients with sporadic PC and may reveal unrecognized HPT-JT. This indicates that CDC73 mutations are major driver mutations in the etiology of PCs. However, there is no genotype-phenotype correlation and some CDC73 mutations (e.g., c.679_680insAG) have been reported in patients with sporadic PC, HPT-JT, or FIHP. Other genes involved in sporadic PC include germline MEN1 and rearranged during transfection (RET) mutations and somatic alterations of the retinoblastoma 1 (RB1) and tumor protein P53 (TP53) genes, as well as epigenetic modifications including DNA methylation and histone modifications, and microRNA misregulation. This review summarizes the genetics and epigenetics of the familial syndromic and non-syndromic (sporadic) forms of PC.
Collapse
Affiliation(s)
- Luís Cardoso
- Department of EndocrinologyDiabetes and MetabolismCentro Hospitalar e Universitário de CoimbraPraceta Prof Mota PintoCoimbraPortugal
- Radcliffe Department of MedicineAcademic Endocrine UnitOxford Centre for DiabetesEndocrinology and MetabolismUniversity of OxfordOxfordUnited Kingdom
| | - Mark Stevenson
- Radcliffe Department of MedicineAcademic Endocrine UnitOxford Centre for DiabetesEndocrinology and MetabolismUniversity of OxfordOxfordUnited Kingdom
| | - Rajesh V. Thakker
- Radcliffe Department of MedicineAcademic Endocrine UnitOxford Centre for DiabetesEndocrinology and MetabolismUniversity of OxfordOxfordUnited Kingdom
| |
Collapse
|
428
|
Chia R, Chiò A, Traynor BJ. Novel genes associated with amyotrophic lateral sclerosis: diagnostic and clinical implications. Lancet Neurol 2017; 17:94-102. [PMID: 29154141 DOI: 10.1016/s1474-4422(17)30401-5] [Citation(s) in RCA: 375] [Impact Index Per Article: 53.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 10/05/2017] [Accepted: 10/05/2017] [Indexed: 12/12/2022]
Abstract
BACKGROUND The disease course of amyotrophic lateral sclerosis (ALS) is rapid and, because its pathophysiology is unclear, few effective treatments are available. Genetic research aims to understand the underlying mechanisms of ALS and identify potential therapeutic targets. The first gene associated with ALS was SOD1, identified in 1993 and, by early 2014, more than 20 genes had been identified as causative of, or highly associated with, ALS. These genetic discoveries have identified key disease pathways that are therapeutically testable and could potentially lead to the development of better treatments for people with ALS. RECENT DEVELOPMENTS Since 2014, seven additional genes have been associated with ALS (MATR3, CHCHD10, TBK1, TUBA4A, NEK1, C21orf2, and CCNF), all of which were identified by genome-wide association studies, whole genome studies, or exome sequencing technologies. Each of the seven novel genes code for proteins associated with one or more molecular pathways known to be involved in ALS. These pathways include dysfunction in global protein homoeostasis resulting from abnormal protein aggregation or a defect in the protein clearance pathway, mitochondrial dysfunction, altered RNA metabolism, impaired cytoskeletal integrity, altered axonal transport dynamics, and DNA damage accumulation due to defective DNA repair. Because these novel genes share common disease pathways with other genes implicated in ALS, therapeutics targeting these pathways could be useful for a broad group of patients stratified by genotype. However, the effects of these novel genes have not yet been investigated in animal models, which will be a key step to translating these findings into clinical practice. WHERE NEXT?: The identification of these seven novel genes has been important in unravelling the molecular mechanisms underlying ALS. However, our understanding of what causes ALS is not complete, and further genetic research will provide additional detail about its causes. Increased genetic knowledge will also identify potential therapeutic targets and could lead to the development of individualised medicine for patients with ALS. These developments will have a direct effect on clinical practice when genome sequencing becomes a routine and integral part of disease diagnosis and management.
Collapse
Affiliation(s)
- Ruth Chia
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA.
| | - Adriano Chiò
- Rita Levi Montalcini Department of Neuroscience, University of Turin, Turin, Italy; Città della Salute e della Scienza University Hospital, Turin, Italy
| | - Bryan J Traynor
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA; Department of Neurology, Brain Sciences Institute, Johns Hopkins Hospital, Baltimore, MD, USA
| |
Collapse
|
429
|
Newey PJ, Berg JN, Zhou K, Palmer CNA, Thakker RV. Utility of Population-Level DNA Sequence Data in the Diagnosis of Hereditary Endocrine Disease. J Endocr Soc 2017; 1:1507-1526. [PMID: 29308445 PMCID: PMC5740525 DOI: 10.1210/js.2017-00330] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 11/10/2017] [Indexed: 12/20/2022] Open
Abstract
Context Genetic testing is increasingly used for clinical diagnosis, although variant interpretation presents a major challenge because of high background rates of rare coding-region variation, which may contribute to inaccurate estimates of variant pathogenicity and disease penetrance. Objective To use the Exome Aggregation Consortium (ExAC) data set to determine the background population frequencies of rare germline coding-region variants in genes associated with hereditary endocrine disease and to evaluate the clinical utility of these data. Design Setting Participants Cumulative frequencies of rare nonsynonymous single-nucleotide variants were established for 38 endocrine disease genes in 60,706 unrelated control individuals. The utility of gene-level and variant-level metrics of tolerability was assessed, and the pathogenicity and penetrance of germline variants previously associated with endocrine disease evaluated. Results The frequency of rare coding-region variants differed markedly between genes and was correlated with the degree of evolutionary conservation. Genes associated with dominant monogenic endocrine disorders typically harbored fewer rare missense and/or loss-of-function variants than expected. In silico variant prediction tools demonstrated low clinical specificity. The frequency of several endocrine disease‒associated variants in the ExAC cohort far exceeded estimates of disease prevalence, indicating either misclassification or overestimation of disease penetrance. Finally, we illustrate how rare variant frequencies may be used to anticipate expected rates of background rare variation when performing disease-targeted genetic testing. Conclusions Quantifying the frequency and spectrum of rare variation using population-level sequence data facilitates improved estimates of variant pathogenicity and penetrance and should be incorporated into the clinical decision-making algorithm when undertaking genetic testing.
Collapse
Affiliation(s)
- Paul J Newey
- Division of Molecular & Clinical Medicine, Ninewells Hospital & Medical School, University of Dundee, Dundee, DD1 9SY, Scotland, United Kingdom
| | - Jonathan N Berg
- Clinical Genetics, Ninewells Hospital & Medical School, University of Dundee, Dundee, DD1 9SY Scotland, United Kingdom
| | - Kaixin Zhou
- Division of Molecular & Clinical Medicine, Ninewells Hospital & Medical School, University of Dundee, Dundee, DD1 9SY, Scotland, United Kingdom
| | - Colin N A Palmer
- Division of Molecular & Clinical Medicine, Ninewells Hospital & Medical School, University of Dundee, Dundee, DD1 9SY, Scotland, United Kingdom
| | - Rajesh V Thakker
- Academic Endocrine Unit, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 7LJ United Kingdom
| |
Collapse
|
430
|
Smagarinsky Y, Burns C, Spinks C, Semsarian C, Ingles J. Development of a communication aid for explaining hypertrophic cardiomyopathy genetic test results. Pilot Feasibility Stud 2017; 3:53. [PMID: 29152326 PMCID: PMC5680798 DOI: 10.1186/s40814-017-0205-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 10/31/2017] [Indexed: 01/10/2023] Open
Abstract
Background Large gene panels are now commonplace for hypertrophic cardiomyopathy (HCM), increasing the yield of uncertain genetic findings. Few resources exist which aim to facilitate communication of HCM genetic test results. We sought to develop, pilot, and refine a communication aid for probands receiving HCM genetic test results. Methods Development was a multi-step process involving expertise of a multidisciplinary team, literature review, and empirical experience. The aid went through an iterative revision process throughout the piloting phase to incorporate feedback. HCM probands attending a specialized multidisciplinary HCM clinic, aged ≥ 18 years and genetic test results available for disclosure between May and August 2016, or recently received their gene results (January–April 2015) were eligible. A purposive sampling strategy was employed, recruiting those attending clinic during the study period or those who could attend without difficulty. Results We developed and pilot tested a genetic counsellor-led communication aid. Based on clinical expertise, the aid addresses (a) what genetic testing is, (b) implications for the patient, (c) reasoning for variant classification, and (d) implications for the family. Pilot data were sought to assess knowledge, feasibility, and acceptability using a self-report survey 2 weeks post-intervention. Twelve of 13 participants completed the follow-up questionnaire. Participants valued the individualised nature of the aid, recommended use of the aid, and indicated genetic knowledge, and family communication was better facilitated. Iterative modification of images helped to more simply depict important genetic concepts. Conclusions We have developed a tool that is feasible, acceptable, and helpful to patients receiving genetic results. This is an important first step, and trial of the aid to assess effectiveness compared to usual care will follow.
Collapse
Affiliation(s)
- Yana Smagarinsky
- Agnes Ginges Centre for Molecular Cardiology, Centenary Institute, Sydney, Australia.,Sydney Medical School, University of Sydney, Sydney, Australia
| | - Charlotte Burns
- Agnes Ginges Centre for Molecular Cardiology, Centenary Institute, Sydney, Australia.,Sydney Medical School, University of Sydney, Sydney, Australia.,Department of Cardiology, Royal Prince Alfred Hospital, Sydney, Australia
| | - Catherine Spinks
- Agnes Ginges Centre for Molecular Cardiology, Centenary Institute, Sydney, Australia.,Department of Cardiology, Royal Prince Alfred Hospital, Sydney, Australia
| | - Christopher Semsarian
- Agnes Ginges Centre for Molecular Cardiology, Centenary Institute, Sydney, Australia.,Sydney Medical School, University of Sydney, Sydney, Australia.,Department of Cardiology, Royal Prince Alfred Hospital, Sydney, Australia
| | - Jodie Ingles
- Agnes Ginges Centre for Molecular Cardiology, Centenary Institute, Sydney, Australia.,Sydney Medical School, University of Sydney, Sydney, Australia.,Department of Cardiology, Royal Prince Alfred Hospital, Sydney, Australia
| |
Collapse
|
431
|
Rueda M, Wagner JL, Phillips TC, Topol SE, Muse ED, Lucas JR, Wagner GN, Topol EJ, Torkamani A. Molecular Autopsy for Sudden Death in the Young: Is Data Aggregation the Key? Front Cardiovasc Med 2017; 4:72. [PMID: 29181379 PMCID: PMC5694161 DOI: 10.3389/fcvm.2017.00072] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Accepted: 10/27/2017] [Indexed: 12/18/2022] Open
Abstract
The Scripps molecular autopsy study seeks to incorporate genetic testing into the postmortem examination of cases of sudden death in the young (<45 years old). Here, we describe the results from the first 2 years of the study, which consisted of whole exome sequencing (WES) of a cohort of 50 cases predominantly from San Diego County. Apart from the individual description of cases, we analyzed the data at the cohort-level, which brought new perspectives on the genetic causes of sudden death. We investigated the advantages and disadvantages of using WES compared to a gene panel for cardiac disease (usually the first genetic test used by medical examiners). In an attempt to connect complex clinical phenotypes with genotypes, we classified samples by their genetic fingerprint. Finally, we studied the benefits of analyzing the mitochondrial DNA genome. In this regard, we found that half of the cases clinically diagnosed as sudden infant death syndrome had an increased ratio of heteroplasmic variants, and that the variants were also present in the mothers. We believe that community-based data aggregation and sharing will eventually lead to an improved classification of variants. Allele frequencies for the all cases can be accessed via our genomics browser at https://genomics.scripps.edu/browser.
Collapse
Affiliation(s)
- Manuel Rueda
- The Scripps Translational Science Institute, Scripps Health, The Scripps Research Institute, La Jolla, CA, United States
| | - Jennifer L Wagner
- The Scripps Translational Science Institute, Scripps Health, The Scripps Research Institute, La Jolla, CA, United States
| | - Tierney C Phillips
- The Scripps Translational Science Institute, Scripps Health, The Scripps Research Institute, La Jolla, CA, United States
| | - Sarah E Topol
- The Scripps Translational Science Institute, Scripps Health, The Scripps Research Institute, La Jolla, CA, United States
| | - Evan D Muse
- The Scripps Translational Science Institute, Scripps Health, The Scripps Research Institute, La Jolla, CA, United States.,Division of Cardiology, Scripps Clinic, La Jolla, CA, United States
| | - Jonathan R Lucas
- Medical Examiner Department, San Diego County, San Diego, CA, United States
| | - Glenn N Wagner
- Medical Examiner Department, San Diego County, San Diego, CA, United States
| | - Eric J Topol
- The Scripps Translational Science Institute, Scripps Health, The Scripps Research Institute, La Jolla, CA, United States.,Division of Cardiology, Scripps Clinic, La Jolla, CA, United States
| | - Ali Torkamani
- The Scripps Translational Science Institute, Scripps Health, The Scripps Research Institute, La Jolla, CA, United States
| |
Collapse
|
432
|
Ehsan M, Jiang H, L Thomson K, Gehmlich K. When signalling goes wrong: pathogenic variants in structural and signalling proteins causing cardiomyopathies. J Muscle Res Cell Motil 2017; 38:303-316. [PMID: 29119312 PMCID: PMC5742121 DOI: 10.1007/s10974-017-9487-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 10/28/2017] [Indexed: 12/20/2022]
Abstract
Cardiomyopathies are a diverse group of cardiac disorders with distinct phenotypes, depending on the proteins and pathways affected. A substantial proportion of cardiomyopathies are inherited and those will be the focus of this review article. With the wide application of high-throughput sequencing in the practice of clinical genetics, the roles of novel genes in cardiomyopathies are recognised. Here, we focus on a subgroup of cardiomyopathy genes [TTN, FHL1, CSRP3, FLNC and PLN, coding for Titin, Four and a Half LIM domain 1, Muscle LIM Protein, Filamin C and Phospholamban, respectively], which, despite their diverse biological functions, all have important signalling functions in the heart, suggesting that disturbances in signalling networks can contribute to cardiomyopathies.
Collapse
Affiliation(s)
- Mehroz Ehsan
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine and British Heart Foundation Centre of Research Excellence, University of Oxford, Oxford, UK
| | - He Jiang
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine and British Heart Foundation Centre of Research Excellence, University of Oxford, Oxford, UK
| | - Kate L Thomson
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine and British Heart Foundation Centre of Research Excellence, University of Oxford, Oxford, UK
| | - Katja Gehmlich
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine and British Heart Foundation Centre of Research Excellence, University of Oxford, Oxford, UK.
| |
Collapse
|
433
|
Fernández MV, Kim JH, Budde JP, Black K, Medvedeva A, Saef B, Deming Y, Del-Aguila J, Ibañez L, Dube U, Harari O, Norton J, Chasse R, Morris JC, Goate A, Cruchaga C. Analysis of neurodegenerative Mendelian genes in clinically diagnosed Alzheimer Disease. PLoS Genet 2017; 13:e1007045. [PMID: 29091718 PMCID: PMC5683650 DOI: 10.1371/journal.pgen.1007045] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 11/13/2017] [Accepted: 09/27/2017] [Indexed: 12/12/2022] Open
Abstract
Alzheimer disease (AD), Frontotemporal lobar degeneration (FTD), Amyotrophic lateral sclerosis (ALS) and Parkinson disease (PD) have a certain degree of clinical, pathological and molecular overlap. Previous studies indicate that causative mutations in AD and FTD/ALS genes can be found in clinical familial AD. We examined the presence of causative and low frequency coding variants in the AD, FTD, ALS and PD Mendelian genes, in over 450 families with clinical history of AD and over 11,710 sporadic cases and cognitive normal participants from North America. Known pathogenic mutations were found in 1.05% of the sporadic cases, in 0.69% of the cognitively normal participants and in 4.22% of the families. A trend towards enrichment, albeit non-significant, was observed for most AD, FTD and PD genes. Only PSEN1 and PINK1 showed consistent association with AD cases when we used ExAC as the control population. These results suggest that current study designs may contain heterogeneity and contamination of the control population, and that current statistical methods for the discovery of novel genes with real pathogenic variants in complex late onset diseases may be inadequate or underpowered to identify genes carrying pathogenic mutations.
Collapse
Affiliation(s)
- Maria Victoria Fernández
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, United States of America
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Jong Hun Kim
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, United States of America
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, United States of America
- Department of Neurology, Dementia Center, Ilsan hospital, National Health Insurance Service, Goyang, South Korea
| | - John P. Budde
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, United States of America
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Kathleen Black
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, United States of America
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Alexandra Medvedeva
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, United States of America
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Ben Saef
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, United States of America
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Yuetiva Deming
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, United States of America
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Jorge Del-Aguila
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, United States of America
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Laura Ibañez
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, United States of America
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Umber Dube
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, United States of America
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, United States of America
- Medical Scientist Training Program, Division of Biology and Biomedical sciences, School of Medicine, Washington University in Saint Louis, St. Louis, MO, United States of America
| | - Oscar Harari
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, United States of America
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Joanne Norton
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, United States of America
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Rachel Chasse
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, United States of America
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, United States of America
| | - John C. Morris
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, United States of America
- Knight Alzheimer's Disease Research Center, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Alison Goate
- Ronald M. Loeb Center for Alzheimer’s disease, Dept of Neuroscience, Icahn School of Medicine at Mount Sinai, ICAHN 10–52, New York, NY, United States of America
| | | | | | - Carlos Cruchaga
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, United States of America
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, United States of America
- * E-mail:
| |
Collapse
|
434
|
McDonald MA, Ashley EA, Fedak PW, Hawkins N, Januzzi JL, McMurray JJ, Parikh VN, Rao V, Svystonyuk D, Teerlink JR, Virani S. Mind the Gap: Current Challenges and Future State of Heart Failure Care. Can J Cardiol 2017; 33:1434-1449. [DOI: 10.1016/j.cjca.2017.08.023] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 08/30/2017] [Accepted: 08/30/2017] [Indexed: 11/24/2022] Open
|
435
|
Kaltman JR, Evans F, Fu YP. Re-evaluating pathogenicity of variants associated with the long QT syndrome. J Cardiovasc Electrophysiol 2017; 29:98-104. [PMID: 28988457 DOI: 10.1111/jce.13355] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 08/17/2017] [Accepted: 09/11/2017] [Indexed: 01/06/2023]
Abstract
INTRODUCTION Genetic testing for congenital long QT syndrome (LQTS) has become common. Recent studies have shown that some variants labelled as pathogenic might be misclassified due to sparse case reports and relatively common allele frequencies (AF) in the general population. This study aims to evaluate the presence of LQTS-associated variants in the Genome Aggregation Database (gnomAD) population, and assess the functional impact of these variants. METHODS AND RESULTS Variants associated with LQTS from the Human Gene Mutation Database were extracted and matched to the gnomAD to evaluate population-based AF. We used MetaSVM to predict the function of LQTS variants. Allele distribution by protein topology in KCNQ1, KCNH2, and SCN5A was compared between gnomAD (n = 123,136) and a cohort of LQTS patients aggregated from eight published studies (n = 2,683). Among the 1,415 LQTS-associated single nucleotide variants in 30 genes, 347 (25%) are present in gnomAD; 24% of the 347 variants were predicted as functionally tolerated compared with 4% of variants not present in gnomAD (P < 0.001). Of the 347 pathogenic variants in gnomAD, seven (2%) had an AF of ≥ 0.001 and 65 (19%) variants had an AF of ≥ 0.0001. In KCNQ1, KCNH2, and SCN5A, allele distribution by protein functional region was significantly different with gnomAD alleles appearing less frequently in highly pathogenic domains than case alleles. CONCLUSION A significant number of LQTS variants have insufficient evidence for pathogenicity and relatively common AF in the general population. Caution should be used when ascribing pathogenicity to these variants.
Collapse
Affiliation(s)
- Jonathan R Kaltman
- Division of Cardiovascular Sciences, National Heart, Lung, and Blood Institute, Bethesda, MD, USA
| | - Frank Evans
- Division of Cardiovascular Sciences, National Heart, Lung, and Blood Institute, Bethesda, MD, USA
| | - Yi-Ping Fu
- Division of Cardiovascular Sciences, National Heart, Lung, and Blood Institute, Bethesda, MD, USA
| |
Collapse
|
436
|
Vora NL, Powell B, Brandt A, Strande N, Hardisty E, Gilmore K, Foreman AKM, Wilhelmsen K, Bizon C, Reilly J, Owen P, Powell CM, Skinner D, Rini C, Lyerly AD, Boggess KA, Weck K, Berg JS, Evans JP. Prenatal exome sequencing in anomalous fetuses: new opportunities and challenges. Genet Med 2017; 19:1207-1216. [PMID: 28518170 PMCID: PMC5675748 DOI: 10.1038/gim.2017.33] [Citation(s) in RCA: 119] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 02/04/2017] [Indexed: 12/13/2022] Open
Abstract
PurposeWe investigated the diagnostic and clinical performance of exome sequencing in fetuses with sonographic abnormalities with normal karyotype and microarray and, in some cases, normal gene-specific sequencing.MethodsExome sequencing was performed on DNA from 15 anomalous fetuses and from the peripheral blood of their parents. Parents provided consent to be informed of diagnostic results in the fetus, medically actionable findings in the parents, and their identification as carrier couples for significant autosomal recessive conditions. We assessed the perceptions and understanding of exome sequencing using mixed methods in 15 mother-father dyads.ResultsIn seven (47%) of 15 fetuses, exome sequencing provided a diagnosis or possible diagnosis with identification of variants in the following genes: COL1A1, MUSK, KCTD1, RTTN, TMEM67, PIEZO1 and DYNC2H1. One additional case revealed a de novo nonsense mutation in a novel candidate gene (MAP4K4). The perceived likelihood that exome sequencing would explain the results (5.2 on a 10-point scale) was higher than the approximately 30% diagnostic yield discussed in pretest counseling.ConclusionExome sequencing had diagnostic utility in a highly select population of fetuses where a genetic diagnosis was highly suspected. Challenges related to genetics literacy and variant interpretation must be addressed by highly tailored pre- and posttest genetic counseling.
Collapse
Affiliation(s)
- Neeta L. Vora
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Bradford Powell
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Alicia Brandt
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Natasha Strande
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Emily Hardisty
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Kelly Gilmore
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Ann Katherine M. Foreman
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
- North Carolina Translational and Clinical Sciences (NC TraCS) Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Kirk Wilhelmsen
- Departments of Genetics and Neurology, Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Chris Bizon
- Departments of Genetics and Neurology, Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Jason Reilly
- Departments of Genetics and Neurology, Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Phil Owen
- Departments of Genetics and Neurology, Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Cynthia M. Powell
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Pediatrics, Division of Genetics and Metabolism, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Debra Skinner
- FPG Child Development Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Christine Rini
- Department of Health Behavior, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Anne D. Lyerly
- Department of Social Medicine and Center for Bioethics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Kim A. Boggess
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Karen Weck
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Jonathan S. Berg
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - James P. Evans
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Social Medicine and Center for Bioethics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| |
Collapse
|
437
|
Minikel EV, MacArthur DG. Publicly Available Data Provide Evidence against NR1H3 R415Q Causing Multiple Sclerosis. Neuron 2017; 92:336-338. [PMID: 27764668 DOI: 10.1016/j.neuron.2016.09.054] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 08/02/2016] [Accepted: 09/20/2016] [Indexed: 10/20/2022]
Abstract
It has recently been reported that an NR1H3 missense variant, R415Q, causes a novel familial form of multiple sclerosis (Wang et al., 2016a). This claim is at odds with publicly available data from the Exome Aggregation Consortium (ExAC; http://exac.broadinstitute.org). The allele frequency of R415Q is not significantly higher in cases (0.024%-0.049%) than in ExAC population controls (0.031%), whereas if R415Q conferred even 50% lifetime risk of developing MS, it would be hundreds of times more common in cases than in controls. The upper bound of the 95% confidence interval of penetrance for R415Q can be estimated at 2.2% for women and 1.2% for men, indicating that even if this variant is disease associated, individuals harboring the variant would have a lifetime risk of developing MS no higher than a few percent. ExAC data should be considered when evaluating claims of variant pathogenicity. This Matters Arising paper is in response to Wang et al. (2016a), published in Neuron. See also the related Matters Arising paper by The International Multiple Sclerosis Genetics Consortium (2016) and the response by Wang et al. (2016b), published in this issue.
Collapse
Affiliation(s)
- Eric Vallabh Minikel
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA 02115, USA.
| | - Daniel G MacArthur
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| |
Collapse
|
438
|
Roos A, Thompson R, Horvath R, Lochmüller H, Sickmann A. Intersection of Proteomics and Genomics to "Solve the Unsolved" in Rare Disorders such as Neurodegenerative and Neuromuscular Diseases. Proteomics Clin Appl 2017; 12. [PMID: 29059504 DOI: 10.1002/prca.201700073] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 07/30/2017] [Indexed: 01/10/2023]
Abstract
Despite recent rapid advances in sequencing technologies, a significant proportion of patients with rare genetic disorders do not receive a genetic diagnosis after exhaustive testing, and even fewer have a potential therapeutic target identified. Taking rare neuromuscular and neurodegenerative disorders as a paradigm that can be extended to other rare Mendelian disorders, this viewpoint explores the opportunities that are brought about by the integration of genomics and proteomics, as well as the limitations and remaining challenges of this newly emerging field of proteogenomics. The relevance of combining proteomic findings with genetic results for diagnosis and gene discovery is illustrated, highlighting the insights the combined analysis provides into the underlying biology and aetiology as well as the limitations of the experimental techniques. A final discussion focuses on the importance of mechanisms to enable the sharing, reuse, and analysis of source experimental data and describes some of the international initiatives that are making progress in this area.
Collapse
Affiliation(s)
- Andreas Roos
- John Walton Muscular Dystrophy Research Centre, International Centre for Life, Institute of Genetic Medicine, Newcastle upon Tyne, England, UK.,Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Dortmund, Germany
| | - Rachel Thompson
- John Walton Muscular Dystrophy Research Centre, International Centre for Life, Institute of Genetic Medicine, Newcastle upon Tyne, England, UK
| | - Rita Horvath
- John Walton Muscular Dystrophy Research Centre, International Centre for Life, Institute of Genetic Medicine, Newcastle upon Tyne, England, UK
| | - Hanns Lochmüller
- John Walton Muscular Dystrophy Research Centre, International Centre for Life, Institute of Genetic Medicine, Newcastle upon Tyne, England, UK
| | - Albert Sickmann
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Dortmund, Germany.,Department of Chemistry, College of Physical Sciences, University of Aberdeen, Aberdeen, Scotland, UK.,Medizinisches Proteom-Center (MPC), Ruhr-Universitat Bochum, Bochum, Germany
| |
Collapse
|
439
|
|
440
|
Cirino AL, Lakdawala NK, McDonough B, Conner L, Adler D, Weinfeld M, O'Gara P, Rehm HL, Machini K, Lebo M, Blout C, Green RC, MacRae CA, Seidman CE, Ho CY. A Comparison of Whole Genome Sequencing to Multigene Panel Testing in Hypertrophic Cardiomyopathy Patients. CIRCULATION. CARDIOVASCULAR GENETICS 2017. [PMID: 29030401 DOI: 10.1161/circgenetics.117.001768.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND As DNA sequencing costs decline, genetic testing options have expanded. Whole exome sequencing and whole genome sequencing (WGS) are entering clinical use, posing questions about their incremental value compared with disease-specific multigene panels that have been the cornerstone of genetic testing. METHODS AND RESULTS Forty-one patients with hypertrophic cardiomyopathy who had undergone targeted hypertrophic cardiomyopathy genetic testing (either multigene panel or familial variant test) were recruited into the MedSeq Project, a clinical trial of WGS. Results from panel genetic testing and WGS were compared. In 20 of 41 participants, panel genetic testing identified variants classified as pathogenic, likely pathogenic, or uncertain significance. WGS identified 19 of these 20 variants, but the variant detection algorithm missed a pathogenic 18 bp duplication in myosin binding protein C (MYBPC3) because of low coverage. In 3 individuals, WGS identified variants in genes implicated in cardiomyopathy but not included in prior panel testing: a pathogenic protein tyrosine phosphatase, non-receptor type 11 (PTPN11) variant and variants of uncertain significance in integrin-linked kinase (ILK) and filamin-C (FLNC). WGS also identified 84 secondary findings (mean=2 per person, range=0-6), which mostly defined carrier status for recessive conditions. CONCLUSIONS WGS detected nearly all variants identified on panel testing, provided 1 new diagnostic finding, and allowed interrogation of posited disease genes. Several variants of uncertain clinical use and numerous secondary genetic findings were also identified. Whereas panel testing and WGS provided similar diagnostic yield, WGS offers the advantage of reanalysis over time to incorporate advances in knowledge, but requires expertise in genomic interpretation to appropriately incorporate WGS into clinical care. CLINICAL TRIAL REGISTRATION URL: https://clinicaltrials.gov. Unique identifier: NCT01736566.
Collapse
Affiliation(s)
- Allison L Cirino
- From the Cardiovascular Division (A.L.C., N.K.L., B.M., D.A., M.W., P.O., C.A.M., C.E.S., C.Y.H.), Department of Pathology (H.L.R.), and Division of Genetics (C.B., R.C.G., C.A.M.), Brigham and Women's Hospital, Boston, MA; Harvard Medical School, Boston, MA (N.K.L., B.M., D.A., M.W., P.O., H.L.R., R.C.G., C.A.M., C.E.S., C.Y.H.); Albany Medical College, NY (L.C.); Broad Institute of Harvard and MIT, Cambridge, MA (H.L.R., R.C.G., C.A.M.); Laboratory for Molecular Medicine (H.L.R., K.M., M.L.), Leadership Team (R.C.G.), Partners HealthCare Personalized Medicine, Cambridge, MA; and Howard Hughes Medical Institute, Chevy Chase, MD (C.E.S.)
| | - Neal K Lakdawala
- From the Cardiovascular Division (A.L.C., N.K.L., B.M., D.A., M.W., P.O., C.A.M., C.E.S., C.Y.H.), Department of Pathology (H.L.R.), and Division of Genetics (C.B., R.C.G., C.A.M.), Brigham and Women's Hospital, Boston, MA; Harvard Medical School, Boston, MA (N.K.L., B.M., D.A., M.W., P.O., H.L.R., R.C.G., C.A.M., C.E.S., C.Y.H.); Albany Medical College, NY (L.C.); Broad Institute of Harvard and MIT, Cambridge, MA (H.L.R., R.C.G., C.A.M.); Laboratory for Molecular Medicine (H.L.R., K.M., M.L.), Leadership Team (R.C.G.), Partners HealthCare Personalized Medicine, Cambridge, MA; and Howard Hughes Medical Institute, Chevy Chase, MD (C.E.S.)
| | - Barbara McDonough
- From the Cardiovascular Division (A.L.C., N.K.L., B.M., D.A., M.W., P.O., C.A.M., C.E.S., C.Y.H.), Department of Pathology (H.L.R.), and Division of Genetics (C.B., R.C.G., C.A.M.), Brigham and Women's Hospital, Boston, MA; Harvard Medical School, Boston, MA (N.K.L., B.M., D.A., M.W., P.O., H.L.R., R.C.G., C.A.M., C.E.S., C.Y.H.); Albany Medical College, NY (L.C.); Broad Institute of Harvard and MIT, Cambridge, MA (H.L.R., R.C.G., C.A.M.); Laboratory for Molecular Medicine (H.L.R., K.M., M.L.), Leadership Team (R.C.G.), Partners HealthCare Personalized Medicine, Cambridge, MA; and Howard Hughes Medical Institute, Chevy Chase, MD (C.E.S.)
| | - Lauren Conner
- From the Cardiovascular Division (A.L.C., N.K.L., B.M., D.A., M.W., P.O., C.A.M., C.E.S., C.Y.H.), Department of Pathology (H.L.R.), and Division of Genetics (C.B., R.C.G., C.A.M.), Brigham and Women's Hospital, Boston, MA; Harvard Medical School, Boston, MA (N.K.L., B.M., D.A., M.W., P.O., H.L.R., R.C.G., C.A.M., C.E.S., C.Y.H.); Albany Medical College, NY (L.C.); Broad Institute of Harvard and MIT, Cambridge, MA (H.L.R., R.C.G., C.A.M.); Laboratory for Molecular Medicine (H.L.R., K.M., M.L.), Leadership Team (R.C.G.), Partners HealthCare Personalized Medicine, Cambridge, MA; and Howard Hughes Medical Institute, Chevy Chase, MD (C.E.S.)
| | - Dale Adler
- From the Cardiovascular Division (A.L.C., N.K.L., B.M., D.A., M.W., P.O., C.A.M., C.E.S., C.Y.H.), Department of Pathology (H.L.R.), and Division of Genetics (C.B., R.C.G., C.A.M.), Brigham and Women's Hospital, Boston, MA; Harvard Medical School, Boston, MA (N.K.L., B.M., D.A., M.W., P.O., H.L.R., R.C.G., C.A.M., C.E.S., C.Y.H.); Albany Medical College, NY (L.C.); Broad Institute of Harvard and MIT, Cambridge, MA (H.L.R., R.C.G., C.A.M.); Laboratory for Molecular Medicine (H.L.R., K.M., M.L.), Leadership Team (R.C.G.), Partners HealthCare Personalized Medicine, Cambridge, MA; and Howard Hughes Medical Institute, Chevy Chase, MD (C.E.S.)
| | - Mark Weinfeld
- From the Cardiovascular Division (A.L.C., N.K.L., B.M., D.A., M.W., P.O., C.A.M., C.E.S., C.Y.H.), Department of Pathology (H.L.R.), and Division of Genetics (C.B., R.C.G., C.A.M.), Brigham and Women's Hospital, Boston, MA; Harvard Medical School, Boston, MA (N.K.L., B.M., D.A., M.W., P.O., H.L.R., R.C.G., C.A.M., C.E.S., C.Y.H.); Albany Medical College, NY (L.C.); Broad Institute of Harvard and MIT, Cambridge, MA (H.L.R., R.C.G., C.A.M.); Laboratory for Molecular Medicine (H.L.R., K.M., M.L.), Leadership Team (R.C.G.), Partners HealthCare Personalized Medicine, Cambridge, MA; and Howard Hughes Medical Institute, Chevy Chase, MD (C.E.S.)
| | - Patrick O'Gara
- From the Cardiovascular Division (A.L.C., N.K.L., B.M., D.A., M.W., P.O., C.A.M., C.E.S., C.Y.H.), Department of Pathology (H.L.R.), and Division of Genetics (C.B., R.C.G., C.A.M.), Brigham and Women's Hospital, Boston, MA; Harvard Medical School, Boston, MA (N.K.L., B.M., D.A., M.W., P.O., H.L.R., R.C.G., C.A.M., C.E.S., C.Y.H.); Albany Medical College, NY (L.C.); Broad Institute of Harvard and MIT, Cambridge, MA (H.L.R., R.C.G., C.A.M.); Laboratory for Molecular Medicine (H.L.R., K.M., M.L.), Leadership Team (R.C.G.), Partners HealthCare Personalized Medicine, Cambridge, MA; and Howard Hughes Medical Institute, Chevy Chase, MD (C.E.S.)
| | - Heidi L Rehm
- From the Cardiovascular Division (A.L.C., N.K.L., B.M., D.A., M.W., P.O., C.A.M., C.E.S., C.Y.H.), Department of Pathology (H.L.R.), and Division of Genetics (C.B., R.C.G., C.A.M.), Brigham and Women's Hospital, Boston, MA; Harvard Medical School, Boston, MA (N.K.L., B.M., D.A., M.W., P.O., H.L.R., R.C.G., C.A.M., C.E.S., C.Y.H.); Albany Medical College, NY (L.C.); Broad Institute of Harvard and MIT, Cambridge, MA (H.L.R., R.C.G., C.A.M.); Laboratory for Molecular Medicine (H.L.R., K.M., M.L.), Leadership Team (R.C.G.), Partners HealthCare Personalized Medicine, Cambridge, MA; and Howard Hughes Medical Institute, Chevy Chase, MD (C.E.S.)
| | - Kalotina Machini
- From the Cardiovascular Division (A.L.C., N.K.L., B.M., D.A., M.W., P.O., C.A.M., C.E.S., C.Y.H.), Department of Pathology (H.L.R.), and Division of Genetics (C.B., R.C.G., C.A.M.), Brigham and Women's Hospital, Boston, MA; Harvard Medical School, Boston, MA (N.K.L., B.M., D.A., M.W., P.O., H.L.R., R.C.G., C.A.M., C.E.S., C.Y.H.); Albany Medical College, NY (L.C.); Broad Institute of Harvard and MIT, Cambridge, MA (H.L.R., R.C.G., C.A.M.); Laboratory for Molecular Medicine (H.L.R., K.M., M.L.), Leadership Team (R.C.G.), Partners HealthCare Personalized Medicine, Cambridge, MA; and Howard Hughes Medical Institute, Chevy Chase, MD (C.E.S.)
| | - Matthew Lebo
- From the Cardiovascular Division (A.L.C., N.K.L., B.M., D.A., M.W., P.O., C.A.M., C.E.S., C.Y.H.), Department of Pathology (H.L.R.), and Division of Genetics (C.B., R.C.G., C.A.M.), Brigham and Women's Hospital, Boston, MA; Harvard Medical School, Boston, MA (N.K.L., B.M., D.A., M.W., P.O., H.L.R., R.C.G., C.A.M., C.E.S., C.Y.H.); Albany Medical College, NY (L.C.); Broad Institute of Harvard and MIT, Cambridge, MA (H.L.R., R.C.G., C.A.M.); Laboratory for Molecular Medicine (H.L.R., K.M., M.L.), Leadership Team (R.C.G.), Partners HealthCare Personalized Medicine, Cambridge, MA; and Howard Hughes Medical Institute, Chevy Chase, MD (C.E.S.)
| | - Carrie Blout
- From the Cardiovascular Division (A.L.C., N.K.L., B.M., D.A., M.W., P.O., C.A.M., C.E.S., C.Y.H.), Department of Pathology (H.L.R.), and Division of Genetics (C.B., R.C.G., C.A.M.), Brigham and Women's Hospital, Boston, MA; Harvard Medical School, Boston, MA (N.K.L., B.M., D.A., M.W., P.O., H.L.R., R.C.G., C.A.M., C.E.S., C.Y.H.); Albany Medical College, NY (L.C.); Broad Institute of Harvard and MIT, Cambridge, MA (H.L.R., R.C.G., C.A.M.); Laboratory for Molecular Medicine (H.L.R., K.M., M.L.), Leadership Team (R.C.G.), Partners HealthCare Personalized Medicine, Cambridge, MA; and Howard Hughes Medical Institute, Chevy Chase, MD (C.E.S.)
| | - Robert C Green
- From the Cardiovascular Division (A.L.C., N.K.L., B.M., D.A., M.W., P.O., C.A.M., C.E.S., C.Y.H.), Department of Pathology (H.L.R.), and Division of Genetics (C.B., R.C.G., C.A.M.), Brigham and Women's Hospital, Boston, MA; Harvard Medical School, Boston, MA (N.K.L., B.M., D.A., M.W., P.O., H.L.R., R.C.G., C.A.M., C.E.S., C.Y.H.); Albany Medical College, NY (L.C.); Broad Institute of Harvard and MIT, Cambridge, MA (H.L.R., R.C.G., C.A.M.); Laboratory for Molecular Medicine (H.L.R., K.M., M.L.), Leadership Team (R.C.G.), Partners HealthCare Personalized Medicine, Cambridge, MA; and Howard Hughes Medical Institute, Chevy Chase, MD (C.E.S.)
| | - Calum A MacRae
- From the Cardiovascular Division (A.L.C., N.K.L., B.M., D.A., M.W., P.O., C.A.M., C.E.S., C.Y.H.), Department of Pathology (H.L.R.), and Division of Genetics (C.B., R.C.G., C.A.M.), Brigham and Women's Hospital, Boston, MA; Harvard Medical School, Boston, MA (N.K.L., B.M., D.A., M.W., P.O., H.L.R., R.C.G., C.A.M., C.E.S., C.Y.H.); Albany Medical College, NY (L.C.); Broad Institute of Harvard and MIT, Cambridge, MA (H.L.R., R.C.G., C.A.M.); Laboratory for Molecular Medicine (H.L.R., K.M., M.L.), Leadership Team (R.C.G.), Partners HealthCare Personalized Medicine, Cambridge, MA; and Howard Hughes Medical Institute, Chevy Chase, MD (C.E.S.)
| | - Christine E Seidman
- From the Cardiovascular Division (A.L.C., N.K.L., B.M., D.A., M.W., P.O., C.A.M., C.E.S., C.Y.H.), Department of Pathology (H.L.R.), and Division of Genetics (C.B., R.C.G., C.A.M.), Brigham and Women's Hospital, Boston, MA; Harvard Medical School, Boston, MA (N.K.L., B.M., D.A., M.W., P.O., H.L.R., R.C.G., C.A.M., C.E.S., C.Y.H.); Albany Medical College, NY (L.C.); Broad Institute of Harvard and MIT, Cambridge, MA (H.L.R., R.C.G., C.A.M.); Laboratory for Molecular Medicine (H.L.R., K.M., M.L.), Leadership Team (R.C.G.), Partners HealthCare Personalized Medicine, Cambridge, MA; and Howard Hughes Medical Institute, Chevy Chase, MD (C.E.S.)
| | - Carolyn Y Ho
- From the Cardiovascular Division (A.L.C., N.K.L., B.M., D.A., M.W., P.O., C.A.M., C.E.S., C.Y.H.), Department of Pathology (H.L.R.), and Division of Genetics (C.B., R.C.G., C.A.M.), Brigham and Women's Hospital, Boston, MA; Harvard Medical School, Boston, MA (N.K.L., B.M., D.A., M.W., P.O., H.L.R., R.C.G., C.A.M., C.E.S., C.Y.H.); Albany Medical College, NY (L.C.); Broad Institute of Harvard and MIT, Cambridge, MA (H.L.R., R.C.G., C.A.M.); Laboratory for Molecular Medicine (H.L.R., K.M., M.L.), Leadership Team (R.C.G.), Partners HealthCare Personalized Medicine, Cambridge, MA; and Howard Hughes Medical Institute, Chevy Chase, MD (C.E.S.).
| | | |
Collapse
|
441
|
Oliver KE, Han ST, Sorscher EJ, Cutting GR. Transformative therapies for rare CFTR missense alleles. Curr Opin Pharmacol 2017; 34:76-82. [PMID: 29032041 DOI: 10.1016/j.coph.2017.09.018] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2017] [Revised: 09/22/2017] [Accepted: 09/26/2017] [Indexed: 01/09/2023]
Abstract
With over 1900 variants reported in the cystic fibrosis transmembrane conductance regulator (CFTR), enhanced understanding of cystic fibrosis (CF) genotype-phenotype correlation represents an important and expanding area of research. The potentiator Ivacaftor has proven an effective treatment for a subset of individuals carrying missense variants, particularly those that impact CFTR gating. Therapeutic efforts have recently focused on correcting the basic defect resulting from the common F508del variant, as well as many less frequent missense alleles. Modest enhancement of F508del-CFTR function has been achieved by combining Ivacaftor with Lumacaftor, a compound that aids maturational processing of misfolded CFTR. Continued development of in silico and in vitro models will facilitate CFTR variant characterization and drug testing, thereby elucidating heterogeneity in the molecular pathogenesis, phenotype, and modulator responsiveness of CF.
Collapse
Affiliation(s)
- Kathryn E Oliver
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA; Children's Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Sangwoo T Han
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Eric J Sorscher
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA; Children's Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Garry R Cutting
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
| |
Collapse
|
442
|
Abstract
Nonischemic dilated cardiomyopathy (DCM) often has a genetic pathogenesis. Because of the large number of genes and alleles attributed to DCM, comprehensive genetic testing encompasses ever-increasing gene panels. Genetic diagnosis can help predict prognosis, especially with regard to arrhythmia risk for certain subtypes. Moreover, cascade genetic testing in family members can identify those who are at risk or with early stage disease, offering the opportunity for early intervention. This review will address diagnosis and management of DCM, including the role of genetic evaluation. We will also overview distinct genetic pathways linked to DCM and their pathogenetic mechanisms. Historically, cardiac morphology has been used to classify cardiomyopathy subtypes. Determining genetic variants is emerging as an additional adjunct to help further refine subtypes of DCM, especially where arrhythmia risk is increased, and ultimately contribute to clinical management.
Collapse
Affiliation(s)
- Elizabeth M McNally
- From the Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago IL (E.M.M.); and Cardiovascular Institute, University of Colorado Anschutz Medical Campus, Aurora (L.M.).
| | - Luisa Mestroni
- From the Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago IL (E.M.M.); and Cardiovascular Institute, University of Colorado Anschutz Medical Campus, Aurora (L.M.).
| |
Collapse
|
443
|
Marian AJ, Braunwald E. Hypertrophic Cardiomyopathy: Genetics, Pathogenesis, Clinical Manifestations, Diagnosis, and Therapy. Circ Res 2017; 121:749-770. [PMID: 28912181 DOI: 10.1161/circresaha.117.311059] [Citation(s) in RCA: 734] [Impact Index Per Article: 104.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Hypertrophic cardiomyopathy (HCM) is a genetic disorder that is characterized by left ventricular hypertrophy unexplained by secondary causes and a nondilated left ventricle with preserved or increased ejection fraction. It is commonly asymmetrical with the most severe hypertrophy involving the basal interventricular septum. Left ventricular outflow tract obstruction is present at rest in about one third of the patients and can be provoked in another third. The histological features of HCM include myocyte hypertrophy and disarray, as well as interstitial fibrosis. The hypertrophy is also frequently associated with left ventricular diastolic dysfunction. In the majority of patients, HCM has a relatively benign course. However, HCM is also an important cause of sudden cardiac death, particularly in adolescents and young adults. Nonsustained ventricular tachycardia, syncope, a family history of sudden cardiac death, and severe cardiac hypertrophy are major risk factors for sudden cardiac death. This complication can usually be averted by implantation of a cardioverter-defibrillator in appropriate high-risk patients. Atrial fibrillation is also a common complication and is not well tolerated. Mutations in over a dozen genes encoding sarcomere-associated proteins cause HCM. MYH7 and MYBPC3, encoding β-myosin heavy chain and myosin-binding protein C, respectively, are the 2 most common genes involved, together accounting for ≈50% of the HCM families. In ≈40% of HCM patients, the causal genes remain to be identified. Mutations in genes responsible for storage diseases also cause a phenotype resembling HCM (genocopy or phenocopy). The routine applications of genetic testing and preclinical identification of family members represents an important advance. The genetic discoveries have enhanced understanding of the molecular pathogenesis of HCM and have stimulated efforts designed to identify new therapeutic agents.
Collapse
Affiliation(s)
- Ali J Marian
- From the Center for Cardiovascular Genetics, Institute of Molecular Medicine, Department of Medicine, University of Texas Health Sciences Center at Houston (A.J.M.); Texas Heart Institute, Houston (A.J.M.); and TIMI Study Group, Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (E.B.).
| | - Eugene Braunwald
- From the Center for Cardiovascular Genetics, Institute of Molecular Medicine, Department of Medicine, University of Texas Health Sciences Center at Houston (A.J.M.); Texas Heart Institute, Houston (A.J.M.); and TIMI Study Group, Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (E.B.)
| |
Collapse
|
444
|
Yang S, Lincoln SE, Kobayashi Y, Nykamp K, Nussbaum RL, Topper S. Sources of discordance among germ-line variant classifications in ClinVar. Genet Med 2017; 19:1118-1126. [PMID: 28569743 PMCID: PMC5632819 DOI: 10.1038/gim.2017.60] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 03/31/2017] [Indexed: 02/02/2023] Open
Abstract
PurposeClinVar is increasingly used as a resource for both genetic variant interpretation and clinical practice. However, controversies exist regarding the consistency of classifications in ClinVar, and questions remain about how best to use these data. Our study systematically examined ClinVar to identify common sources of discordance and thus inform ongoing practices.MethodsWe analyzed variants that had multiple classifications in ClinVar, excluding benign polymorphisms. Classifications were categorized by potential actionability and pathogenicity. Consensus interpretations were calculated for each variant, and the properties of the discordant outlier classifications were summarized.ResultsOur study included 74,065 classifications of 27,224 unique variants in 1,713 genes. We found that (i) concordance rates differed among clinical areas and variant types; (ii) clinical testing methods had much higher concordance than basic literature curation and research efforts; (iii) older classifications had greater discordance than newer ones; and (iv) low-penetrance variants had particularly high discordance.ConclusionRecent variant classifications from clinical testing laboratories have high overall concordance in many (but not all) clinical areas. ClinVar can be a reliable resource supporting variant interpretation, quality assessment, and clinical practice when factors uncovered in this study are taken into account. Ongoing improvements to ClinVar may make it easier to use, particularly for nonexpert users.
Collapse
Affiliation(s)
- Shan Yang
- Invitae, San Francisco, California, USA
| | | | | | | | - Robert L Nussbaum
- Invitae, San Francisco, California, USA
- Volunteer Clinical Faculty, University of California, San Francisco, California, USA
| | | |
Collapse
|
445
|
Déraspe M, Raymond F, Boisvert S, Culley A, Roy PH, Laviolette F, Corbeil J. Phenetic Comparison of Prokaryotic Genomes Using k-mers. Mol Biol Evol 2017; 34:2716-2729. [PMID: 28957508 PMCID: PMC5850840 DOI: 10.1093/molbev/msx200] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Bacterial genomics studies are getting more extensive and complex, requiring new ways to envision analyses. Using the Ray Surveyor software, we demonstrate that comparison of genomes based on their k-mer content allows reconstruction of phenetic trees without the need of prior data curation, such as core genome alignment of a species. We validated the methodology using simulated genomes and previously published phylogenomic studies of Streptococcus pneumoniae and Pseudomonas aeruginosa. We also investigated the relationship of specific genetic determinants with bacterial population structures. By comparing clusters from the complete genomic content of a genome population with clusters from specific functional categories of genes, we can determine how the population structures are correlated. Indeed, the strain clustering based on a subset of k-mers allows determination of its similarity with the whole genome clusters. We also applied this methodology on 42 species of bacteria to determine the correlational significance of five important bacterial genomic characteristics. For example, intrinsic resistance is more important in P. aeruginosa than in S. pneumoniae, and the former has increased correlation of its population structure with antibiotic resistance genes. The global view of the pangenome of bacteria also demonstrated the taxa-dependent interaction of population structure with antibiotic resistance, bacteriophage, plasmid, and mobile element k-mer data sets.
Collapse
Affiliation(s)
- Maxime Déraspe
- Centre de Recherche en Infectiologie, CHU de Québec-Université Laval, Quebec City, QC, Canada
- Centre de Recherche en Données Massives de l’Université Laval, Quebec City, QC, Canada
- Département de Médecine Moléculaire, Université Laval, Quebec City, QC, Canada
| | - Frédéric Raymond
- Centre de Recherche en Infectiologie, CHU de Québec-Université Laval, Quebec City, QC, Canada
- Centre de Recherche en Données Massives de l’Université Laval, Quebec City, QC, Canada
| | | | - Alexander Culley
- Département de Biochimie, Microbiologie et Bio-informatique, Université Laval, Quebec City, QC, Canada
| | - Paul H. Roy
- Centre de Recherche en Infectiologie, CHU de Québec-Université Laval, Quebec City, QC, Canada
- Département de Biochimie, Microbiologie et Bio-informatique, Université Laval, Quebec City, QC, Canada
| | - François Laviolette
- Centre de Recherche en Données Massives de l’Université Laval, Quebec City, QC, Canada
- Département d’Informatique et de Génie Logiciel, Université Laval, Quebec City, QC, Canada
| | - Jacques Corbeil
- Centre de Recherche en Infectiologie, CHU de Québec-Université Laval, Quebec City, QC, Canada
- Centre de Recherche en Données Massives de l’Université Laval, Quebec City, QC, Canada
- Département de Médecine Moléculaire, Université Laval, Quebec City, QC, Canada
| |
Collapse
|
446
|
Kassem HS, Walsh R, Barton PJ, Abdelghany BS, Azer RS, Buchan R, John S, Elguindy A, Moharem-ElGamal S, Badran HM, Shehata H, Cook SA, Yacoub MH. A comparative study of mutation screening of sarcomeric genes ( MYBPC3 , MYH7 , TNNT2 ) using single gene approach versus targeted gene panel next generation sequencing in a cohort of HCM patients in Egypt. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2017. [DOI: 10.1016/j.ejmhg.2017.05.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
|
447
|
Abstract
PURPOSE OF REVIEW Paediatric cardiomyopathy is a rare disease with a genetic basis. The purpose of this review is to discuss the current status of genetic findings in the paediatric cardiomyopathy population and present recent progress in utilizing this information for management and therapy. RECENT FINDINGS With increased clinical genetic testing, an understanding of the genetic causes of cardiomyopathy is improving and novel causes are identified at a rapid rate. Recent progress in identifying the scope of genetic variation in large population datasets has led to reassessment and refinement of our understanding of the significance of rare genetic variation. As a result, the stringency of variant interpretation has increased, at times leading to revision of previous mutation results. Transcriptome and epigenome studies are elucidating important pathways for disease progression and highlight similarities and differences in pathogenesis from adult cardiomyopathy. Therapy targeted towards the underlying cause of cardiomyopathy is emerging for a number of rare syndromes such as Pompe and Noonan syndromes, and genome editing and induced pluripotent stem cells provide promise for additional precision medicine approaches. SUMMARY Genetics is moving at a rapid pace in paediatric cardiomyopathy. Genetic testing is increasingly being incorporated into clinical care. Although interpretation of rare genetic variation remains challenging, the opportunity to provide management and therapy targeted towards the underlying genetic cause is beginning to be realized.
Collapse
Affiliation(s)
- Stephanie M. Ware
- Departments of Pediatrics and Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN
| |
Collapse
|
448
|
Lacaze P, Ryan J, Woods R, Winship I, McNeil J. Pathogenic variants in the healthy elderly: unique ethical and practical challenges. JOURNAL OF MEDICAL ETHICS 2017; 43:714-722. [PMID: 28341755 PMCID: PMC5629947 DOI: 10.1136/medethics-2016-103967] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 12/20/2016] [Accepted: 02/06/2017] [Indexed: 05/06/2023]
Abstract
: Genetic research into ageing, longevity and late-onset disease is becoming increasingly common. Yet, there is a paucity of knowledge related to clinical actionability and the return of pathogenic variants to otherwise healthy elderly individuals. Whether or not genetic research in the elderly should be managed differently from standard practices adapted for younger populations has not yet been defined. In this article, we provide an overview of ethical and practical challenges in preparing for a genetic study of over 14 000 healthy Australians aged 70 years or older enrolled in the ASPirin in Reducing Events in the Elderly (ASPREE) Healthy Ageing Biobank. At the time of consent, all participants in this study were free of life-threatening illness, cardiovascular disease or cognitive impairment. ASPREE is thus a cohort of healthy elderly individuals with seemingly minimal burden of genetic disease recruited without ascertainment bias. The cohort presents a unique opportunity to address the penetrance of known pathogenic variants in a population without disease symptoms; however, it also raises a number of ethical concerns regarding the interpretation and disclosure of variants with known clinical actionability. Some of the challenges include (a) how to manage the interpretation, disclosure and actioning of pathogenic variants found in otherwise healthy elderly adults without disease symptoms, (b) whether or not to disclose findings for the benefit of family members rather than elderly consented donors themselves, (c) how to manage the return of genetic findings to the elderly individuals who are now in severe cognitive decline or terminal illness, (d) how to ensure quality of information and clinical service upon disclosure of results to this demographic and (e) how to prepare for the insurance implications of disclosing genetic information under Australian law. We discuss these and other dilemmas and propose a defensible plan of management. TRIAL REGISTRATION NUMBER ISRCTN83772183.
Collapse
Affiliation(s)
- Paul Lacaze
- Department of Epidemiology and Preventive Medicine, School of Public Health and Preventive Medicine, ASPREE - Monash University, Melbourne, Victoria, Australia
| | - Joanne Ryan
- Department of Epidemiology and Preventive Medicine, School of Public Health and Preventive Medicine, ASPREE - Monash University, Melbourne, Victoria, Australia
| | - Robyn Woods
- Department of Epidemiology and Preventive Medicine, School of Public Health and Preventive Medicine, ASPREE - Monash University, Melbourne, Victoria, Australia
| | - Ingrid Winship
- Genetic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Melbourne, Victoria, Australia
- Department of Medicine, University of Melbourne, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - John McNeil
- Department of Epidemiology and Preventive Medicine, School of Public Health and Preventive Medicine, ASPREE - Monash University, Melbourne, Victoria, Australia
| |
Collapse
|
449
|
Adam S, Friedman JM. Controversy and debate on clinical genomics sequencing-paper 4: clinical genome-wide sequencing: response to Wilson, Miller, and Rousseau. J Clin Epidemiol 2017; 92:13-15. [PMID: 28951108 DOI: 10.1016/j.jclinepi.2017.09.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Shelin Adam
- Department of Medical Genetics, University of British Columbia, C328 - 4500 Oak Street, Vancouver, British Columbia V6H 3V4, Canada.
| | - Jan M Friedman
- Department of Medical Genetics, University of British Columbia, C328 - 4500 Oak Street, Vancouver, British Columbia V6H 3V4, Canada
| |
Collapse
|
450
|
Kanduri C, Domanska D, Hovig E, Sandve GK. Genome build information is an essential part of genomic track files. Genome Biol 2017; 18:175. [PMID: 28911336 PMCID: PMC5599886 DOI: 10.1186/s13059-017-1312-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 08/29/2017] [Indexed: 11/10/2022] Open
Abstract
Genomic locations are represented as coordinates on a specific genome build version, but the build information is frequently missing when coordinates are provided. We show that this information is essential to correctly interpret and analyse the genomic intervals contained in genomic track files. Although not a substitute for best practices, we also provide a tool to predict the genome build version of genomic track files.
Collapse
Affiliation(s)
- Chakravarthi Kanduri
- Department of Informatics, University of Oslo, 0316, Oslo, Norway
- K.G. Jebsen Coeliac Disease Research Centre, University of Oslo, 0318, Oslo, Norway
| | - Diana Domanska
- Department of Informatics, University of Oslo, 0316, Oslo, Norway
| | - Eivind Hovig
- Department of Informatics, University of Oslo, 0316, Oslo, Norway
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, 0424, Oslo, Norway
- Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, 0424, Oslo, Norway
| | - Geir Kjetil Sandve
- Department of Informatics, University of Oslo, 0316, Oslo, Norway.
- K.G. Jebsen Coeliac Disease Research Centre, University of Oslo, 0318, Oslo, Norway.
| |
Collapse
|